Commit 3639fda3 authored by Lena Hersemann's avatar Lena Hersemann

removed bug; cosmetics

parent 9440a74e
......@@ -13,7 +13,7 @@ Quality control and filtering of scRNAseq data
Usage: sc_quality_check.R <folder_with_star_counts_matrices_and_design>
'
# commandArgs <- function(x) c("metrices")
# commandArgs <- function(x) c("metrices_subsetted")
opts = docopt(doc, commandArgs(TRUE))
......@@ -93,11 +93,10 @@ sce <- lapply(setNames(names(sce), names(sce)), function(x) {
})
#'<br><br>
#' ## Check for sequencing saturation
#' ## Check sequencing saturation
#' The following saturation plot of the invidivudal cells is based on the sequencing depth of per cell as well as higher
#' and lower simulated sequencing depths. For this plot all features with a counts > 0 were taken into account.
lapply(setNames(names(sce), names(sce)), function(x){
x = "SC2"
dat <- readData(data = counts(sce[[x]]), factors = colData(sce[[x]]))
mysaturation = dat(dat, k = 0, ndepth = 7, type = "saturation")
sat_data <- dat2save(mysaturation)
......@@ -117,7 +116,7 @@ lapply(setNames(names(sce), names(sce)), function(x){
#'<br><br>
#' ## Check cell's library sizes
#' ## Check library size
#' The library size is defined by the sum of all counts per cell and corresponds to the number of reads mapped to the reference genome
#' <br>
lapply(names(sce), function(x){
......@@ -130,7 +129,7 @@ lapply(names(sce), function(x){
# grid.arrange(grobs = ., nrow = plot_rows, heights=unit(0.5, "npc"))
#' <br><br>
#' ## Check cell's number of expressed genes
#' ## Check number of expressed genes
#' The number of expressed genes corresponds to the number of genes per cell with an actual count (i.e. > 0)
#' <br>
lapply(names(sce), function(x){
......
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