Package {tinyarray}

auto_geo_group

Description

Infer sample groups from GEO phenotype metadata.

Usage

auto_geo_group(
  x,
  group_col = "title",
  choice = NULL,
  min_group_size = 2L,
  max_groups = 20L,
  min_coverage = 0.8,
  search_other_cols = TRUE,
  stopwords = .tinyarray_geo_stopwords(),
  levels = NULL,
  ref = NULL,
  verbose = TRUE
)

Arguments

Details

The function first tries the user-specified 'group_col', then 'title'. If no stable grouping is found, it scans the remaining columns and returns a table of candidate groupings for manual selection. Both binary and multigroup factors are supported. Rare groups are left as 'NA' rather than being relabeled as another group.

Labels that differ only in capitalization are merged, retaining their most common spelling. Shared affixes and trailing sample identifiers are removed when they can be identified consistently.

Value

A list with 'group_list', 'source_col', 'selected_index', 'candidate_table', 'candidates', and 'pdata'.

Examples

pd <- data.frame(
  title = c("Control sample", "Control sample", "Treat sample", "Treat sample"),
  stringsAsFactors = FALSE
)
rownames(pd) <- paste0("s", 1:4)
res <- auto_geo_group(
  pd,
  choice = 1,
  levels = c("Control", "Treat"),
  ref = "Control",
  verbose = FALSE
)
res$source_col
levels(res$group_list)
table(res$group_list)

box_surv

Description

draw box plot for a hub gene expression matrix

Usage

box_surv(
  exp_hub,
  exprSet_hub,
  meta,
  xlab = "Group",
  ylab = "Expression",
  p.label = FALSE
)

Arguments

Value

patchwork result for hub genes boxplot and survival plot

Author(s)

Xiaojie Sun

See Also

exp_boxplot;exp_surv

Examples

k = box_surv(log2(exp_hub1+1),exprSet_hub1,meta1);k[[1]]

cod

Description

Example TCGA expression matrix used in grouping and plotting demos.

Usage

cod

Format

An object of class matrix (inherits from array) with 100 rows and 512 columns.

Examples

  cod

cor.test for all variables

Description

cor.test for all variables(each two columns)

Usage

cor.full(x, drop = min(x, na.rm = TRUE) - 0.001, min.obs = 10)

Arguments

Value

a data.frame with cor.test p.value and estimate

Author(s)

Xiaojie Sun

See Also

cor.one

Examples

x = iris[,-5]
cor.full(x)

cor.test for one variable with all variables

Description

cor.test for all variables(each two columns)

Usage

cor.one(
  x,
  var,
  drop.var = min(x[, var], na.rm = TRUE) - 0.001,
  drop.other = min(x[, -which(colnames(x) == var)], na.rm = TRUE) - 0.001,
  min.obs = 10
)

Arguments

Value

A data.frame with cor.test p.value and estimate

Author(s)

Xiaojie Sun

See Also

cor.full

Examples

x = iris[,-5]
cor.one(x,"Sepal.Width")

corheatmap

Description

draw cor heatmap

Usage

corheatmap(exp, x, y, color = c("#2fa1dd", "white", "#f87669"))

Arguments

Value

a ggplot object

Author(s)

Xiaojie Sun

Examples

x = rownames(exprSet_hub1)[1:3]
y = rownames(exprSet_hub1)[4:7]
corheatmap(exprSet_hub1,x,y)

corscatterplot

Description

draw cor scatter plot with density plot by ggplot2

Usage

corscatterplot(
  dat,
  x,
  y,
  color_cor = "blue",
  fill_cor = "lightgray",
  fill_x = "#ff820e",
  fill_y = "#0000fe",
  type = "density",
  ...
)

Arguments

Value

a ggplot object

Author(s)

Xiaojie Sun

Examples

corscatterplot(iris,"Sepal.Length","Sepal.Width")

deg

Description

Example limma differential analysis result for GSE42872.

Usage

deg

Format

An object of class data.frame with 18591 rows and 10 columns.

Examples

  head(deg)

deseq_data

Description

Example DESeq2 differential analysis result.

Usage

deseq_data

Format

An object of class data.frame with 552 rows and 6 columns.

Examples

  head(deseq_data)

draw enrichment bar plots for both up and down genes

Description

draw enrichment bar plots for both up and down genes,for human only.

Usage

double_enrich(deg, n = 10, color = c("#2874C5", "#f87669"), species = "human")

Arguments

Value

a list with kegg and go bar plot according to up and down genes enrichment result.

Author(s)

Xiaojie Sun

See Also

quick_enrich

Examples

## Not run: 
deg = data.frame(
  ENTREZID = genes[1:20],
  change = rep(c("up", "down"), 10)
)
double_enrich(deg)

## End(Not run)

draw_KM

Description

draw KM-plot with two or more group

Usage

draw_KM(
  meta,
  group_list,
  time_col = "time",
  event_col = "event",
  legend.title = "Group",
  legend.labs = NULL,
  color = c("#2874C5", "#f87669", "#e6b707", "#868686", "#92C5DE", "#F4A582", "#66C2A5",
    "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3"),
  ...
)

Arguments

Value

a KM-plot

Author(s)

Xiaojie Sun

Examples

x = survival::lung
draw_KM(meta = x,
       group_list = x$sex,event_col = "status")

draw boxplot for expression

Description

draw boxplot for expression

Usage

draw_boxplot(
  exp,
  group_list,
  method = "kruskal.test",
  sort = TRUE,
  drop = FALSE,
  width = 0.5,
  pvalue_cutoff = 0.05,
  xlab = "Gene",
  ylab = "Expression",
  grouplab = "Group",
  p.label = FALSE,
  add_error_bar = FALSE,
  color = c("#2874C5", "#f87669", "#e6b707", "#868686", "#66C2A5", "#FC8D62", "#8DA0CB",
    "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3"),
  ...
)

Arguments

Value

a boxplot according to exp and grouped by group.

Author(s)

Xiaojie Sun

See Also

draw_heatmap;draw_volcano;draw_venn

Examples

draw_boxplot(t(iris[,1:4]),iris$Species)
exp <-  matrix(rnorm(60),nrow = 10)
colnames(exp) <- paste0("sample",1:6)
rownames(exp) <- paste0("gene",1:10)
exp[,4:6] = exp[,4:6] +10
exp[1:4,1:4]
group_list <- factor(rep(c("A","B"),each = 3))
draw_boxplot(exp,group_list)
draw_boxplot(exp,group_list,color = c("grey","red"))

draw a heatmap plot

Description

draw a heatmap plot for an expression matrix grouped by group_list; if scale = TRUE, the matrix is scaled before plotting.

Usage

draw_heatmap(
  n,
  group_list,
  scale_before = FALSE,
  n_cutoff = 3,
  legend = FALSE,
  show_rownames = FALSE,
  annotation_legend = FALSE,
  split_column = FALSE,
  show_column_title = FALSE,
  color = (grDevices::colorRampPalette(c("#2fa1dd", "white", "#f87669")))(100),
  color_an = c("#2fa1dd", "#f87669", "#e6b707", "#868686", "#92C5DE", "#F4A582",
    "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494",
    "#B3B3B3"),
  scale = TRUE,
  main = NA,
  ...
)

Arguments

Value

a heatmap plot according to n and grouped by group_list.

Author(s)

Xiaojie Sun

See Also

draw_pca;draw_volcano;draw_venn

Examples

#example data
exp = matrix(abs(rnorm(60,sd = 16)),nrow = 10)
exp[,4:6] <- exp[,4:6]+20
colnames(exp) <- paste0("sample",1:6)
rownames(exp) <- paste0("gene",1:10)
exp[1:4,1:4]
group_list = factor(rep(c("A","B"),each = 3))
draw_heatmap(exp,group_list)
#use iris
n = t(iris[,1:4]);colnames(n) = 1:150
group_list = iris$Species
draw_heatmap(n,group_list)
draw_heatmap(n,group_list,color = colorRampPalette(c("green","black","red"))(100),
             color_an = c("red","blue","pink") )

draw heatmap plots

Description

Print heatmap plots for an expression matrix grouped by group_list.

Usage

draw_heatmap2(exp, group_list, deg, my_genes = NULL, heat_union = TRUE, ...)

Arguments

Value

a heatmap plot according to exp and grouped by group_list.

Author(s)

Xiaojie Sun

See Also

draw_pca;draw_volcano;draw_venn

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
  gse = "GSE474"
  geo = geo_download(gse,destdir=tempdir())
  geo$exp[1:4,1:4]
  geo$exp=log2(geo$exp+1)
  group_list=ifelse(stringr::str_detect(geo$pd$title,"MObese"),"MObese",
  ifelse(stringr::str_detect(geo$pd$title,"NonObese"),"NonObese","Obese"))
  group_list=factor(group_list,levels = c("NonObese","Obese","MObese"))
  find_anno(geo$gpl)
  ids <- AnnoProbe::idmap(geo$gpl,destdir = tempdir())
  deg = multi_deg(geo$exp,group_list,ids,adjust = FALSE,entriz = FALSE)
  draw_heatmap2(geo$exp,group_list,deg)
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    warning("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')",call. = FALSE)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    warning("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')",call. = FALSE)
  }
}

## End(Not run)

draw PCA plots

Description

do PCA analysis and warning a PCA plot

Usage

draw_pca(
  exp,
  group_list,
  color = c("#2874C5", "#f87669", "#e6b707", "#868686", "#92C5DE", "#F4A582", "#66C2A5",
    "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3"),
  addEllipses = TRUE,
  style = "default",
  color.label = "Group",
  title = "",
  ...
)

Arguments

Value

a PCA plot according to exp and grouped by group_list.

Author(s)

Xiaojie Sun

See Also

draw_heatmap;draw_volcano;draw_venn

Examples

draw_pca(t(iris[,1:4]),iris$Species)
#change color
draw_pca(t(iris[,1:4]),iris$Species,color = c("#E78AC3", "#A6D854", "#FFD92F"))


draw_pca(t(iris[,1:4]),iris$Species,style = "ggplot2")


draw_pca(t(iris[,1:4]),iris$Species,style = "3D")

draw_tsne

Description

draw tsne plot with annotation by ggplot2

Usage

draw_tsne(
  exp,
  group_list,
  perplexity = 30,
  color = c("#2874C5", "#f87669", "#e6b707", "#868686", "#92C5DE", "#F4A582", "#66C2A5",
    "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3"),
  color.label = "group",
  addEllipses = TRUE
)

Arguments

Value

a ggplot object

Author(s)

Xiaojie Sun

Examples

exp <-  matrix(rnorm(10000),nrow = 50)
colnames(exp) <- paste0("sample",1:200)
rownames(exp) <- paste0("gene",1:50)
exp[1:4,1:4]
exp[,1:100] = exp[,1:100]+10
group_list <- factor(rep(c("A","B"),each = 100))
draw_tsne(exp,group_list)

draw a venn plot

Description

warning a venn plot for deg result created by three packages

Usage

draw_venn(
  x,
  main,
  color = c("#2874C5", "#f87669", "#e6b707", "#868686", "#66C2A5", "#FC8D62", "#8DA0CB",
    "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3"),
  imagetype = "png",
  filename = NULL,
  lwd = 1,
  lty = 1,
  col = color[1:length(x)],
  fill = color[1:length(x)],
  cat.col = color[1:length(x)],
  cat.cex = 1,
  cat.dist = -0.15,
  rotation.degree = 0,
  main.cex = 1,
  cex = 1,
  alpha = 0.1,
  reverse = TRUE,
  ...
)

Arguments

Value

a venn plot according to x, y, and z using the list names as labels.

Author(s)

Xiaojie Sun

See Also

draw_pca;draw_volcano;draw_heatmap

Examples

x = list(Deseq2=sample(1:100,30),edgeR = sample(1:100,30),limma = sample(1:100,30))
draw_venn(x,"test")
draw_venn(x,"test",color = c("darkgreen", "darkblue", "#B2182B"))

draw a volcano plot

Description

warning a volcano plot for Differential analysis result in data.frame format.

Usage

draw_volcano(
  deg,
  lab = NA,
  xlab.package = TRUE,
  pvalue_cutoff = 0.05,
  logFC_cutoff = 1,
  pkg = 1,
  adjust = TRUE,
  change_col = "change",
  symmetry = FALSE,
  color = c("#2874C5", "grey", "#f87669")
)

Arguments

Value

a volcano plot according to logFC and either -log10(P.value) or -log10(padj), depending on adjust.

Author(s)

Xiaojie Sun

See Also

draw_heatmap;draw_pca;draw_venn

Examples

head(deseq_data)
draw_volcano(deseq_data)
draw_volcano(deseq_data,pvalue_cutoff = 0.01,logFC_cutoff = 2)
draw_volcano(deseq_data,color = c("darkgreen", "darkgrey", "#B2182B"))

draw_volcano2

Description

Print one or more volcano plots for differential analysis results in a data.frame.

Usage

draw_volcano2(deg, pkg = 4, lab, change_col = "change", ...)

Arguments

Value

one or more volcano plot

Author(s)

Xiaojie Sun

See Also

geo_download;draw_volcano;draw_venn

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
#two group
gse = "GSE42872"
geo = geo_download(gse,destdir=tempdir())
group_list = rep(c("A","B"),each = 3)
ids = AnnoProbe::idmap('GPL6244',destdir = tempdir())
deg = get_deg(geo$exp,group_list,ids)
draw_volcano2(deg)
#multigroup
gse = "GSE474"
geo = geo_download(gse,destdir=tempdir())
geo$exp[1:4,1:4]
geo$exp=log2(geo$exp+1)
group_list=ifelse(stringr::str_detect(geo$pd$title,"MObese"),"MObese",
ifelse(stringr::str_detect(geo$pd$title,"NonObese"),"NonObese","Obese"))
group_list=factor(group_list,levels = c("NonObese","Obese","MObese"))
find_anno(geo$gpl)
ids <- AnnoProbe::idmap(geo$gpl,destdir = tempdir())
deg = multi_deg(geo$exp,group_list,ids,adjust = FALSE,entriz = FALSE)
draw_volcano2(deg)
draw_volcano2(deg,color = c("darkgreen","grey","darkred"))
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    warning("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')",call. = FALSE)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    warning("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')",call. = FALSE)
  }
}

## End(Not run)

count unique values in every columns for data.frame

Description

in geo analysis,this function can help you simplify pdata, delete columns with unique values,which can't be used as group vector

Usage

dumd(x)

Arguments

Value

The simple data.frame of columns unique values count in x

Examples

dumd(iris)
data(ToothGrowth)
x = ToothGrowth
dumd(ToothGrowth)

edges_to_nodes

Description

get nodes from edges

Usage

edges_to_nodes(edges)

Arguments

Value

nodes data.frame

Author(s)

Xiaojie Sun

See Also

interaction_to_edges

Examples

df = data.frame(a = c("gene1","gene2","gene3"),
b = c("d,f,a,b",
"c,e,g",
"a,b,d"))
edges = interaction_to_edges(df)
nodes = edges_to_nodes(edges)

exists_anno_list

Description

GEO GPL platforms with direct AnnoProbe annotation support.

Usage

exists_anno_list

Format

An object of class character of length 175.

Examples

  exists_anno_list

exp_boxplot

Description

draw box plot for a hub gene expression matrix

Usage

exp_boxplot(
  exp_hub,
  xlab = NULL,
  ylab = NULL,
  p.label = FALSE,
  color = c("#2fa1dd", "#f87669")
)

Arguments

Value

box plots list for all genes in the matrix

Author(s)

Xiaojie Sun

See Also

exp_surv;box_surv

Examples

k = exp_boxplot(log2(exp_hub1+1));k[[1]]

exp_hub1

Description

Example TCGA+GTEx expression matrix.

Usage

exp_hub1

Format

An object of class matrix (inherits from array) with 8 rows and 350 columns.

Examples

  exp_hub1[1:4,1:4]

exp_surv

Description

draw surv plot for a hub gene expression matrix for tumor samples

Usage

exp_surv(exprSet_hub, meta, cut.point = FALSE, color = c("#2874C5", "#f87669"))

Arguments

Value

survival plots list for all genes

Author(s)

Xiaojie Sun

See Also

exp_boxplot;box_surv;draw_venn

Examples

tmp = exp_surv(exprSet_hub1,meta1)
patchwork::wrap_plots(tmp)+patchwork::plot_layout(guides = "collect")
tmp2 = exp_surv(exprSet_hub1,meta1,cut.point = TRUE)
patchwork::wrap_plots(tmp2)+patchwork::plot_layout(guides = "collect")

exprSet_hub1

Description

Example TCGA CPM matrix with tumor samples only.

Usage

exprSet_hub1

Format

An object of class matrix (inherits from array) with 8 rows and 177 columns.

Examples

  exprSet_hub1[1:4,1:4]

Find an annotation table for a GEO platform accession.

Description

The function prints a short explanation plus the code used to obtain annotations. It only tests AnnoProbe 'type' values when no Bioconductor annotation package source exists for the GPL accession.

Usage

find_anno(gpl, install = FALSE, update = FALSE)

Arguments

Value

No return value. The function prints available annotation resources and optionally installs a Bioconductor annotation package.

Author(s)

Xiaojie Sun

See Also

geo_download

Examples

## Not run: 
try(find_anno("GPL570"), silent = TRUE)

## End(Not run)

genes

Description

Small example vector of Entrez IDs.

Usage

genes

Format

An object of class character of length 511.

Examples

  genes

geo_download

Description

Download GEO expression data and return the expression matrix, phenotype data, and platform information.

Usage

geo_download(
  gse,
  by_annopbrobe = TRUE,
  simpd = TRUE,
  colon_remove = TRUE,
  download_timeout = getOption("timeout"),
  destdir = getwd(),
  n = 1
)

Arguments

Details

Cached 'eSet' objects are stored as '.rds' files in 'destdir'; legacy '.Rdata' cache files are still readable, and incomplete cache files will be kept so the download can resume automatically.

Value

a list with 'exp', 'pd', 'gpl', and 'group_candidates', or 'NULL' when the data cannot be read or downloaded

Author(s)

Xiaojie Sun

See Also

find_anno

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)){
  gse = "GSE42872"
  a = geo_download(gse,destdir=tempdir())
}

## End(Not run)

geo_parser

Description

Legacy helper for parsing GEO series matrix files. Prefer [geo_download()] for normal use.

Usage

geo_parser(gse, destdir = getwd())

Arguments

Value

an ExpressionSet object list

Author(s)

Xiaojie Sun

See Also

find_anno

Examples

## Not run: 
gse = "GSE42872"
a = try(geo_parser(gse,destdir=tempdir()), silent = TRUE)

## End(Not run)

get_cgs

Description

extract DEGs from deg data.frame

Usage

get_cgs(deg)

Arguments

Value

a list with upgenes,downgenes,diffgenes.

Author(s)

Xiaojie Sun

See Also

geo_download;draw_volcano;draw_venn

Examples

## Not run: 
#two group
gse = "GSE42872"
geo = geo_download(gse,destdir=tempdir())
group_list = rep(c("A","B"),each = 3)
ids = AnnoProbe::idmap('GPL6244',destdir=tempdir())
deg = get_deg(geo$exp,group_list,ids)
cgs = get_cgs(deg)
#mutigroup
gse = "GSE474"
geo = geo_download(gse,destdir=tempdir())
geo$exp[1:4,1:4]
geo$exp=log2(geo$exp+1)
group_list=ifelse(stringr::str_detect(geo$pd$title,"MObese"),"MObese",
ifelse(stringr::str_detect(geo$pd$title,"NonObese"),"NonObese","Obese"))
group_list=factor(group_list,levels = c("NonObese","Obese","MObese"))
find_anno(geo$gpl)
ids = AnnoProbe::idmap(geo$gpl,destdir = tempdir())
deg = multi_deg(geo$exp,group_list,ids,adjust = FALSE)
cgs = get_cgs(deg)

## End(Not run)

get count from GEO

Description

get RNA-seq count file from GEO database

Usage

get_count_txt(gse, destdir = getwd(), download = FALSE)

Arguments

Value

No return value. When 'download = TRUE', the count file is saved in 'destdir'.

Author(s)

Xiaojie Sun

See Also

geo_download

Examples

get_count_txt("GSE162550",destdir = tempdir())

get_deg

Description

Do differential analysis according to an expression set and group information.

Usage

get_deg(
  exp,
  group_list,
  ids = NULL,
  logFC_cutoff = 1,
  pvalue_cutoff = 0.05,
  adjust = TRUE,
  entriz = TRUE,
  species = "human"
)

Arguments

Value

a deg data.frame

Author(s)

Xiaojie Sun

See Also

multi_deg;get_deg_all

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
  gse = "GSE42872"
  a = geo_download(gse,destdir=tempdir())
  find_anno(geo$gpl)
  ids <- AnnoProbe::idmap(geo$gpl,destdir = tempdir())
  Group = rep(c("control","treat"),each = 3)
  Group = factor(Group)
  deg = get_deg(geo$exp,Group,ids,entriz = FALSE)
  head(deg)
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    warning("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')",call. = FALSE)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    warning("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')",call. = FALSE)
  }
}

## End(Not run)

get_deg_all

Description

Do differential analysis according to an expression set and group information.

Usage

get_deg_all(
  exp,
  group_list,
  ids = NULL,
  symmetry = TRUE,
  my_genes = NULL,
  show_rownames = FALSE,
  cluster_cols = TRUE,
  color_volcano = c("#2874C5", "grey", "#f87669"),
  logFC_cutoff = 1,
  pvalue_cutoff = 0.05,
  adjust = TRUE,
  entriz = TRUE,
  n_cutoff = 2,
  annotation_legend = FALSE,
  lab = NA,
  change_col = "change",
  species = "human"
)

Arguments

Value

a list with a deg data.frame, volcano plot, PCA plot, heatmap, and a list with DEGs.

Author(s)

Xiaojie Sun

See Also

get_deg;multi_deg_all

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
  gse = "GSE42872"
  geo = geo_download(gse,destdir=tempdir())
  group_list = rep(c("A","B"),each = 3)
  group_list = factor(group_list)
  find_anno(geo$gpl)
  ids <- AnnoProbe::idmap(geo$gpl,destdir = tempdir())
  dcp = get_deg_all(geo$exp,group_list,ids,entriz = FALSE)
  head(dcp$deg)
  dcp$plots
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    warning("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')",call. = FALSE)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    warning("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')",call. = FALSE)
  }
}

## End(Not run)

get gpl txt from GEO

Description

get gpl annotation txt file from GEO database

Usage

get_gpl_txt(gpl, destdir = getwd(), download = FALSE)

Arguments

Value

No return value. When 'download = TRUE', the GPL annotation file is saved in 'destdir'.

Author(s)

Xiaojie Sun

See Also

geo_download

Examples

get_gpl_txt("GPL23270",destdir = tempdir())

Get probe-to-symbol ids for a GEO platform accession.

Description

Prefer the available Bioconductor annotation package when possible, and fall back to 'AnnoProbe::idmap()' when no Bioconductor annotation package source exists. The function prints a short explanation plus the code it used.

Usage

get_ids(gpl, type = NULL, install = FALSE, update = FALSE)

Arguments

Value

a cleaned two-column data.frame with 'probe_id' and 'symbol'

Author(s)

Xiaojie Sun

See Also

find_anno

Examples

## Not run: 
get_ids("GPL570")

## End(Not run)

ggheat

Description

draw heatmap plot with annotation by ggplot2

Usage

ggheat(
  dat,
  group,
  cluster = FALSE,
  color = c("#2874C5", "white", "#f87669"),
  legend_color = c("#2874C5", "#f87669", "#e6b707", "#868686", "#66C2A5", "#FC8D62",
    "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3"),
  show_rownames = NULL,
  show_colnames = TRUE,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  groupname = "group",
  expname = "exp",
  fill_mid = TRUE,
  rotate_rownames = NULL
)

Arguments

Value

a ggplot object

Author(s)

Xiaojie Sun

Examples

exp_dat = matrix(sample(100:1000,40),ncol = 4)
exp_dat[1:(nrow(exp_dat)/2),] =  exp_dat[1:(nrow(exp_dat)/2),]-1000
rownames(exp_dat) = paste0("sample",1:nrow(exp_dat))
colnames(exp_dat) = paste0("gene",1:ncol(exp_dat))
group = rep(c("A","B"),each = nrow(exp_dat)/2)
group = factor(group,levels = c("A","B"))
ggheat(exp_dat,group)
ggheat(exp_dat,group,cluster_rows = TRUE)
ggheat(exp_dat,group,cluster_rows = TRUE,show_rownames = FALSE,
       show_colnames = FALSE,groupname = "risk",expname = "expression")

hypertest

Description

make hypertest for given lncRNA and mRNA common miRNAs

Usage

hypertest(lnc, pc, deMIR = NULL, lnctarget, pctarget)

Arguments

Value

a data.frame with hypertest result

Author(s)

Xiaojie Sun

See Also

plcortest

Examples

# to update

interaction_to_edges

Description

Split interactions by 'sep' and return an edges data.frame.

Usage

interaction_to_edges(df, a = 1, b = 2, sep = ",")

Arguments

Value

a new data.frame with two columns, one interaction per row

Author(s)

Xiaojie Sun

See Also

edges_to_nodes

Examples

df = data.frame(a = c("gene1","gene2","gene3"),
b = c("d,f,a,b",
"c,e,g",
"a,b,d"))
interaction_to_edges(df)

intersect_all

Description

calculate intersect set for two or more elements

Usage

intersect_all(...)

Arguments

Value

vector

Author(s)

Xiaojie Sun

See Also

union_all

Examples

x1 = letters[1:4]
x2 = letters[3:6]
x3 = letters[3:4]
re =intersect_all(x1,x2,x3)
re2 = intersect_all(list(x1,x2,x3))
re3 = union_all(x1,x2,x3)

lnc_anno

Description

Compact lncRNA annotation table for TCGA expression matrices.

Usage

lnc_anno

Format

An object of class data.frame with 14852 rows and 2 columns.

Details

Only the columns needed by the package are kept, so the bundled object stays small and can be used offline without extra annotation files.

Examples

  head(lnc_anno)

mRNA_anno

Description

Compact mRNA annotation table for TCGA expression matrices.

Usage

mRNA_anno

Format

An object of class data.frame with 19797 rows and 2 columns.

Details

Only the columns needed by the package are kept, so the bundled object stays small and can be used offline without extra annotation files.

Examples

  head(mRNA_anno)

make_tcga_group

Description

make tcga group for given tcga sample names or expression matrix

Usage

make_tcga_group(exp)

Arguments

Value

a group factor with normal and tumor, corresponding to the sample names

Author(s)

Xiaojie Sun

See Also

sam_filter;match_exp_cl

Examples

k = make_tcga_group(exp_hub1);table(k)
k2 = make_tcga_group(colnames(exp_hub1));table(k2)

match_exp_cl

Description

match exp and clinical data from TCGA

Usage

match_exp_cl(exp, cl, id_column = "id", sample_centric = TRUE)

Arguments

Value

a transformed clinical data.frame with sample ids.

Author(s)

Xiaojie Sun

See Also

make_tcga_group;sam_filter

Examples

a = match_exp_cl(exp_hub1,meta1[,2:4],"X_PATIENT")
exp_matched = a[[1]]
cl_matched = a[[2]]
b = match_exp_cl(exp_hub1,meta1[,2:4],"X_PATIENT",sample_centric = FALSE)
exp_matched = b[[1]]
cl_matched = b[[2]]

meta1

Description

Example clinical table matched to exprSet_hub1.

Usage

meta1

Format

An object of class data.frame with 177 rows and 4 columns.

Examples

  head(meta1)

multi_deg

Description

Do differential analysis according to an expression set and group information.

Usage

multi_deg(
  exp,
  group_list,
  ids = NULL,
  logFC_cutoff = 1,
  pvalue_cutoff = 0.05,
  adjust = TRUE,
  species = "human",
  entriz = TRUE
)

Arguments

Value

a deg data.frame with one element per contrast

Author(s)

Xiaojie Sun

See Also

get_deg;multi_deg_all

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
  gse = "GSE474"
  geo = geo_download(gse,destdir=tempdir())
  geo$exp[1:4,1:4]
  geo$exp=log2(geo$exp+1)
  group_list=ifelse(stringr::str_detect(geo$pd$title,"MObese"),
  "MObese",ifelse(stringr::str_detect(geo$pd$title,"NonObese"),
  "NonObese","Obese"))
  group_list=factor(group_list,levels = c("NonObese","Obese","MObese"))
  find_anno(geo$gpl)
  ids <- AnnoProbe::idmap(geo$gpl,destdir = tempdir())
  deg = multi_deg(geo$exp,group_list,ids,adjust = FALSE,entriz = FALSE)
  names(deg)
  head(deg[[1]])
  head(deg[[2]])
  head(deg[[3]])
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    warning("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')",call. = FALSE)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    warning("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')",call. = FALSE)
  }
}

## End(Not run)

multi_deg_all

Description

Do differential analysis according to an expression set and group information.

Usage

multi_deg_all(
  exp,
  group_list,
  ids = NULL,
  symmetry = TRUE,
  my_genes = NULL,
  show_rownames = FALSE,
  cluster_cols = TRUE,
  color_volcano = c("#2874C5", "grey", "#f87669"),
  pvalue_cutoff = 0.05,
  logFC_cutoff = 1,
  adjust = TRUE,
  entriz = TRUE,
  change_col = "change",
  annotation_legend = FALSE,
  lab = NA,
  species = "human"
)

Arguments

Value

a list with deg data.frame, volcano plot and a list with DEGs.

Author(s)

Xiaojie Sun

See Also

geo_download;draw_volcano;draw_venn

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
gse = "GSE474"
geo = geo_download(gse,destdir=tempdir())
geo$exp[1:4,1:4]
geo$exp=log2(geo$exp+1)
group_list=ifelse(stringr::str_detect(geo$pd$title,"MObese"),"MObese",
ifelse(stringr::str_detect(geo$pd$title,"NonObese"),"NonObese","Obese"))
group_list=factor(group_list,levels = c("NonObese","Obese","MObese"))
find_anno(geo$gpl)
ids = AnnoProbe::idmap(geo$gpl,destdir = tempdir())
dcp = multi_deg_all(geo$exp,
group_list,ids,adjust = FALSE,entriz = FALSE)
dcp[[3]]
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    warning("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')",call. = FALSE)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    warning("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')",call. = FALSE)
  }
}

## End(Not run)

pkg_all

Description

Lookup table for GEO platform annotation packages.

Usage

pkg_all

Format

An object of class data.frame with 82 rows and 3 columns.

Examples

  head(pkg_all)

plcortest

Description

make cor.test for given lncRNA and mRNA

Usage

plcortest(lnc_exp, mRNA_exp, cor_cutoff = 0)

Arguments

Value

a list with cor.test result,names are lncRNAs, element are mRNAs

Author(s)

Xiaojie Sun

See Also

hypertest

Examples

# to update

plot_deg

Description

Plot PCA, volcano, heatmap, and Venn plots for differential analysis results.

Usage

plot_deg(
  exp,
  group_list,
  deg,
  symmetry = TRUE,
  my_genes = NULL,
  show_rownames = FALSE,
  cluster_cols = TRUE,
  color_volcano = c("#2874C5", "grey", "#f87669"),
  pvalue_cutoff = 0.05,
  logFC_cutoff = 1,
  adjust = TRUE,
  change_col = "change",
  annotation_legend = FALSE,
  lab = NA,
  species = "human"
)

Arguments

Value

plots

Author(s)

Xiaojie Sun

Examples

## Not run: 
if(requireNamespace("Biobase",quietly = TRUE)&
   requireNamespace("AnnoProbe",quietly = TRUE)){
gse = "GSE474"
geo = geo_download(gse,destdir=tempdir())
geo$exp[1:4,1:4]
geo$exp=log2(geo$exp+1)
group_list=ifelse(stringr::str_detect(geo$pd$title,"MObese"),"MObese",
ifelse(stringr::str_detect(geo$pd$title,"NonObese"),"NonObese","Obese"))
group_list=factor(group_list,levels = c("NonObese","Obese","MObese"))
find_anno(geo$gpl)
ids = AnnoProbe::idmap(geo$gpl,destdir = tempdir())
deg = get_deg(geo$exp,group_list,ids,adjust = FALSE,entriz = FALSE)
plot_deg(geo$exp,group_list,deg)
}else{
  if(!requireNamespace("AnnoProbe",quietly = TRUE)) {
    warning("Package 'AnnoProbe' needed for this function to work.
         Please install it by install.packages('AnnoProbe')",call. = FALSE)
  }
  if(!requireNamespace("Biobase",quietly = TRUE)) {
    warning("Package 'Biobase' needed for this function to work.
         Please install it by BiocManager::install('Biobase')",call. = FALSE)
  }
}

## End(Not run)

point_cut

Description

calculate cut point for multiple genes

Usage

point_cut(exprSet_hub, meta)

Arguments

Value

a vector with cutpoint for genes

Author(s)

Xiaojie Sun

See Also

surv_KM;surv_cox

Examples

point_cut(exprSet_hub1,meta1)

Print a GEO auto-group result

Description

Print a GEO auto-group result

Usage

## S3 method for class 'geo_auto_group'
print(x, ...)

Arguments

quick_enrich

Description

Perform enrichment analysis for a gene list; human is the default species.

Usage

quick_enrich(genes, kkgo_file = NULL, destdir = getwd(), species = "human")

Arguments

Value

enrichment results and dotplots

Author(s)

Xiaojie Sun

See Also

double_enrich

Examples

## Not run: 
head(genes)
g = quick_enrich(genes,destdir = tempdir())
names(g)
g$kk
g$go

## End(Not run)

risk_plot

Description

draw risk plot

Usage

risk_plot(
  exprSet_hub,
  meta,
  riskscore,
  cut.point = FALSE,
  color = c("#2fa1dd", "#f87669"),
  n_cutoff = 3
)

Arguments

Value

risk plot

Author(s)

Xiaojie Sun

See Also

exp_boxplot;box_surv;draw_venn

Examples

risk_plot(exprSet_hub1,meta1,riskscore = rnorm(nrow(meta1)))

sam_filter

Description

drop duplicated samples from the same patients

Usage

sam_filter(exp)

Arguments

Value

a transformed expression set without duplicated samples

Author(s)

Xiaojie Sun

See Also

make_tcga_group;match_exp_cl

Examples

exp_hub1[1:4,1:4]
dim(exp_hub1)
exp2 = sam_filter(exp_hub1)
dim(exp2)
g = make_tcga_group(exp_hub1);table(g)
table(!duplicated(substr(colnames(exp_hub1[,g=="tumor"]),1,12)))

surv_KM

Description

calculate log_rank test p values for genes

Usage

surv_KM(
  exprSet_hub,
  meta,
  cut.point = FALSE,
  pvalue_cutoff = 0.05,
  min_gn = 0.1
)

Arguments

Value

a vector with gene names and log_rank p value

Author(s)

Xiaojie Sun

See Also

point_cut;surv_cox

Examples

surv_KM(exprSet_hub1,meta1)
surv_KM(exprSet_hub1,meta1,pvalue_cutoff = 1)
surv_KM(exprSet_hub1,meta1,cut.point = TRUE)

surv_cox

Description

calculate cox p values and HR for genes

Usage

surv_cox(
  exprSet_hub,
  meta,
  cut.point = FALSE,
  pvalue_cutoff = 0.05,
  HRkeep = "all",
  continuous = FALSE,
  min_gn = 0.1
)

Arguments

Value

a matrix with gene names ,cox p value and HR

Author(s)

Xiaojie Sun

See Also

point_cut;surv_KM

Examples

surv_cox(exprSet_hub1,meta1)
surv_cox(exprSet_hub1,meta1,cut.point = TRUE,continuous = TRUE)
surv_cox(exprSet_hub1,meta1,cut.point = TRUE,continuous = TRUE,pvalue_cutoff = 1)

t_choose

Description

choose differential expressed genes by simple t.test

Usage

t_choose(
  genes,
  exp,
  group_list,
  up_only = FALSE,
  down_only = FALSE,
  pvalue_cutoff = 0.05
)

Arguments

Value

a vector with differential expressed genes

Author(s)

Xiaojie Sun

Examples

exp = matrix(rnorm(1000),ncol = 10)
rownames(exp) = sample(mRNA_anno$gene_id,100)
colnames(exp) = c(paste0("TCGA",1:5),paste0("GTEX",1:5))
exp2  = trans_exp(exp)
exp2[,1:5] = exp2[,1:5]+10
group_list = rep(c("A","B"),each = 5)
genes = sample(rownames(exp2),3)
t_choose(genes,exp2,group_list)

trans_array

Description

transform rownames for microarray or rnaseq expression matrix

Usage

trans_array(exp, ids, from = "probe_id", to = "symbol", average = FALSE)

Arguments

Value

a transformed expression set with new rownames

Author(s)

Xiaojie Sun

See Also

trans_exp

Examples

exp = matrix(1:50,nrow = 10)
rownames(exp) = paste0("g",1:10)
ids = data.frame(probe_id = paste0("g",1:10),
                symbol = paste0("G",c(1:9,9)))
trans_array(exp,ids)
trans_array(exp,ids,average = TRUE)

trans_ensembl_exp

Description

Transform rownames of an expression set from Ensembl IDs to gene symbols using the latest gene annotation.

Usage

trans_ensembl_exp(
  exp,
  mrna_only = FALSE,
  lncrna_only = FALSE,
  species = "human",
  average = FALSE
)

Arguments

Value

a transformed expression set with symbol

Author(s)

Xiaojie Sun

See Also

trans_exp_new

Examples

exp = matrix(rnorm(1000),ncol = 10)
rownames(exp) = sample(mRNA_anno$gene_id,100)
colnames(exp) = c(paste0("TCGA",1:5),paste0("GTEX",1:5))
k  = trans_ensembl_exp(exp)

trans_entrezexp

Description

Transform rownames of an expression set from Entrez IDs to gene symbols using clusterProfiler::bitr().

Usage

trans_entrezexp(entrezexp, species = "human", average = FALSE)

trans_entrez_exp(entrezexp, species = "human", average = FALSE)

Arguments

Value

a transformed expression set with symbol

Author(s)

Xiaojie Sun

See Also

trans_exp

Examples

exp = matrix(rnorm(200),ncol = 10)
rownames(exp) = c("79691", "56271", "8662", "10394", "55630", "159162", "23541",
                  "79723", "54413", "22927", "92342", "23787", "5550", "8924",
                  "55274", "866", "8844", "353299", "587", "1473")
colnames(exp) = paste0("s",1:10)
exp2 = trans_entrezexp(exp)

trans_exp

Description

Transform rownames of an expression matrix from Ensembl IDs to gene symbols.

Usage

trans_exp(exp, mrna_only = FALSE, lncrna_only = FALSE, gtex = FALSE)

Arguments

Value

a transformed expression set with symbol

Author(s)

Xiaojie Sun

See Also

trans_array

Examples

exp = matrix(rnorm(1000),ncol = 10)
rownames(exp) = sample(mRNA_anno$gene_id,100)
colnames(exp) = paste0("sample",1:10)
k  = trans_exp(exp)

trans_exp_new

Description

Route expression-matrix ID conversion by type.

Usage

trans_exp_new(
  exp,
  mrna_only = FALSE,
  lncrna_only = FALSE,
  species = "human",
  average = FALSE,
  type = c("ensembl", "array", "entrez"),
  ids = NULL,
  id = NULL
)

Arguments

Value

a transformed expression set with symbol

Author(s)

Xiaojie Sun

See Also

trans_ensembl_exp;trans_array;trans_entrezexp

Examples

exp = matrix(rnorm(1000),ncol = 10)
rownames(exp) = sample(mRNA_anno$gene_id,100)
colnames(exp) = c(paste0("TCGA",1:5),paste0("GTEX",1:5))
k  = trans_exp_new(exp)

union_all

Description

calculate union set for two or more elements

Usage

union_all(...)

Arguments

Value

vector

Author(s)

Xiaojie Sun

See Also

intersect_all

Examples

x1 = letters[1:4]
x2 = letters[3:6]
x3 = letters[3:4]
re =intersect_all(x1,x2,x3)
re2 = intersect_all(list(x1,x2,x3))
re3 = union_all(x1,x2,x3)