add

DESCRIPTION

@@ -39,4 +39,3 @@ Suggests:
     Rtsne
 Depends:R (>= 3.5.0)
 RoxygenNote: 7.1.1
-Language: 1en-US

R/1_plots.R

@@ -297,7 +297,7 @@ draw_venn <- function(x,name,color = c("#2874C5","#f87669","#e6b707","#868686","
 ##'
 ##' @inheritParams draw_pca
 ##' @param method one of kruskal.test,aov,t.test and wilcox.test
-##' @param width wdith of boxplot and error bar
+##' @param width width of boxplot and error bar
 ##' @param sort whether the boxplot will be sorted
 ##' @param drop whether to discard insignificant values
 ##' @param pvalue_cutoff if drop = TRUE,genes with p-values below the threshold will be drawn

R/2_geo_id.R

@@ -14,9 +14,11 @@
 ##' @importFrom dplyr %>%
 ##' @export
 ##' @examples
+##' \dontrun{
 ##' gse = "GSE42872"
 ##' a = geo_download(gse,destdir=tempdir())
 ##' b = geo_download(gse,by_annopbrobe = FALSE,destdir=tempdir())
+##' }
 ##' @seealso
 ##' \code{\link{find_anno}}
 

R/6_multi_deg_all.R

@@ -7,6 +7,7 @@
 ##' @author Xiaojie Sun
 ##' @export
 ##' @examples
+##' \dontrun{
 ##' #two group
 ##' gse = "GSE42872"
 ##' geo = geo_download(gse,destdir=tempdir())
@@ -26,6 +27,7 @@
 ##' ids = AnnoProbe::idmap(geo$gpl,destdir = tempdir())
 ##' deg = multi_deg(geo$exp,group_list,ids,adjust = FALSE)
 ##' cgs = get_cgs(deg)
+##' }
 ##' @seealso
 ##' \code{\link{geo_download}};\code{\link{draw_volcano}};\code{\link{draw_venn}}
 
@@ -62,6 +64,7 @@ get_cgs <- function(deg){
 ##' @importFrom patchwork plot_layout
 ##' @export
 ##' @examples
+##' \dontrun{
 ##' #two group
 ##' gse = "GSE42872"
 ##' geo = geo_download(gse,destdir=tempdir())
@@ -82,6 +85,7 @@ get_cgs <- function(deg){
 ##' deg = multi_deg(geo$exp,group_list,ids,adjust = FALSE)
 ##' draw_volcano2(deg)
 ##' draw_volcano2(deg,color = c("darkgreen","grey","darkred"))
+##' }
 ##' @seealso
 ##' \code{\link{geo_download}};\code{\link{draw_volcano}};\code{\link{draw_venn}}
 
@@ -134,6 +138,7 @@ draw_volcano2 = function(deg,
 ##' @importFrom pheatmap pheatmap
 ##' @export
 ##' @examples
+##' \dontrun{
 ##' gse = "GSE474"
 ##' geo = geo_download(gse,destdir=tempdir())
 ##' geo$exp[1:4,1:4]
@@ -145,6 +150,7 @@ draw_volcano2 = function(deg,
 ##' ids <- AnnoProbe::idmap(geo$gpl,destdir = tempdir())
 ##' deg = multi_deg(geo$exp,group_list,ids,adjust = FALSE)
 ##' draw_heatmap2(geo$exp,group_list,deg)
+##' }
 ##' @seealso
 ##' \code{\link{draw_pca}};\code{\link{draw_volcano}};\code{\link{draw_venn}}
 

R/7_quick_double_enrich.R

@@ -17,12 +17,14 @@
 ##' @importFrom ggplot2 scale_x_discrete
 ##' @export
 ##' @examples
+##' \dontrun{
 ##' head(genes)
 ##' g = quick_enrich(genes,destdir = tempdir())
 ##' names(g)
 ##' g[[1]][1:4,1:4]
 ##' g[[3]]
 ##' g[[4]]
+##' }
 ##' @seealso
 ##' \code{\link{double_enrich}}
 
@@ -91,7 +93,9 @@ quick_enrich <- function(genes,
 ##' @importFrom ggplot2 theme
 ##' @export
 ##' @examples
-##' # double_enrich(deg)
+##' \dontrun{
+##' double_enrich(deg)
+##' }
 ##' @seealso
 ##' \code{\link{quick_enrich}}
 

R/8_tcga_group_trans_exp.R

@@ -15,7 +15,7 @@
 
 make_tcga_group <- function(exp){
   k1 = stringr::str_starts(colnames(exp),"TCGA")
-  if(!any(k1))stop("no tcga samples detected,please check it")
+  if(!any(k1))stop("no TCGA samples detected,please check it")
   k2 = suppressWarnings(as.numeric(stringr::str_sub(colnames(exp),14,15))<10)
   group_list = ifelse(k1&k2,"tumor","normal")
   group_list = factor(group_list,levels = c("normal","tumor"))
@@ -24,12 +24,12 @@ make_tcga_group <- function(exp){
 
 ##' trans_exp
 ##'
-##' transform rownames of tcga or tcga_gtex expression set from gdc or xena,from ensembl id to gene symbol
+##' transform rownames of TCGA or TCGA_Gtex expression set from gdc or xena,from ensembl id to gene symbol
 ##'
-##' @param exp tcga or tcga_gtex expression set from gdc or xena
+##' @param exp TCGA or TCGA_Gtex expression set from gdc or xena
 ##' @param mrna_only only keep mrna rows in result
 ##' @param lncrna_only only keep lncrna rows in result
-##' @param gtex logical,whether including gtex data
+##' @param gtex logical,whether including Gtex data
 ##' @return a transformed expression set with symbol
 ##' @author Xiaojie Sun
 ##' @importFrom stringr str_detect
@@ -99,7 +99,7 @@ utils::globalVariables(c("lnc_anno","mRNA_anno","lnc_annov23","mRNA_annov23"))
 ##'
 ##' transform rownames for microarray expression matrix
 ##'
-##' @param exp tcga or tcga_gtex expression set from gdc or xena
+##' @param exp TCGA or TCGA_Gtex expression set from gdc or xena
 ##' @param ids data.frame  with original rownames and new rownames
 ##' @param from colname for original rownames
 ##' @param to colname for new rownames
@@ -133,7 +133,7 @@ trans_array = function(exp,ids,from = "probe_id",
 ##'
 ##' drop duplicated samples from the same patients
 ##'
-##' @param exp tcga or tcga_gtex expression set from gdc or xena
+##' @param exp TCGA or TCGA_Gtex expression set from gdc or xena
 ##' @return a transformed expression set without duplicated samples
 ##' @author Xiaojie Sun
 ##' @export
@@ -166,10 +166,10 @@ sam_filter = function(exp){
 
 ##' match_exp_cl
 ##'
-##' match exp and clinical data from tcga
+##' match exp and clinical data from TCGA
 ##'
-##' @param exp tcga  expression set
-##' @param cl tcga clinical data.frame
+##' @param exp TCGA  expression set
+##' @param cl TCGA clinical data.frame
 ##' @param id_column which column contains patient ids, column number or colnmn name.
 ##' @param sample_centric logical,deault T,keep all samples from the same patients.if FALSE,keep only one tumor sample for one patient.
 ##' @return a transformed clinical data.frame with sample ids.