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| f_TCGA_gleason_grade <- function(primary_gleason_grade, secondary_gleason_grade){
primary_gleason_grade <- as.numeric(unlist(data.frame(strsplit(primary_gleason_grade, ' '))[2,]))
secondary_gleason_grade <- as.numeric(unlist(data.frame(strsplit(secondary_gleason_grade, ' '))[2,]))
primary_gleason_grade + secondary_gleason_grade
}
f_rank_transformation_o <- function(lo){
lo <- unlist(lo)
idx <- order(lo, decreasing = F)
idm <- as.data.frame(table(lo))
idm <- idm[idm$Freq>1, ]
idm <- idm[[1]]
for(i in idm){
ii <- (lo == i)
idx[ii] <- mean(idx[ii])
}
names(idx) <- names(lo)
idx
}
f_SCE_VlnBoxPlot_gD <- function(featureN, assayN='TPM', rank_trans=F, rmZero=NULL, log_trans=T, ...){
sceList <- list(...)
df <- data.frame()
for(name in names(sceList)){
sce <- sceList[[name]]
idx <- rowRanges(sce)$external_gene_name == featureN
tmp <- assay(sce[idx, ], assayN)
tmp <- data.frame(groupN=name, value=tmp[1,])
df <- rbind(df, tmp)
}
if(log_trans){
df$value <- log1p(df$value)
}
if(rank_trans){
df$value <- f_rank_transformation_o(df$value)
df
}else{
if(!is.null(rmZero)){
df[df$value>rmZero, ]
}else{df}
}
}
|