Count_SRRs: Count data and save the result

In ZhenWei10/RbashGEO: GEO raw data processing in bash.

Usage

Count_SRRs(SRRs, bam_dir = "./", reference_annotation, save_title,
  paired = F, Mode = "Union", Ignore.strand = T, Inter.feature = F)

Arguments

SRRs	The bam file names (without .bam).
reference_annotation	A Granges object.
Mode, Inter.feature, Ignore.strand	Default settings are "Union",FALSE, and TRUE resectively; see summarizeOverlaps for more information. Generally, set Ignore.strand = TRUE if you are not using strand specific library (other wise you usually lose half of your data). Set Inter.feature = T if you want to deal with overlapping features.

See Also

Rsamtools_view

Examples

Count_SRRs(SRR_RUN_human_SE,"./",Annotation_gr,F,"Example_human_SE")


###An example to handel a long list of bam files with either single end or paired end sequencing library

library(RbashGEO)

Annot_GR <- GenomicRanges::reduce( readRDS("SVM_RMBase.rds") ,min.gapwidth=0L) 
Coldata_df <- read.csv("Coldata_target_human.csv")
Count_seperately <- function(SRR_RUN,BAM_dir,Annot_gr,title){
 if(sum(!paste0(SRR_RUN,".bam") %in% grep(".bam", list.files(BAM_dir) , value = T)) > 0) {stop("Incomplete bam files, please check again.")}
 SRR_RUN_SE <- as.character( SRR_RUN )[Coldata_df$Lib == "Single"]
 SRR_RUN_PE <- as.character( SRR_RUN )[Coldata_df$Lib == "Paired"]
Count_SRRs(SRR_RUN_SE,BAM_dir,Annot_gr,paste0(title,"_SE"),F)
 Count_SRRs(SRR_RUN_PE,BAM_dir,Annot_gr,paste0(title,"_PE"),T)
}
Count_seperately(Coldata_df$SRR_RUN,"/home/zhen/TREW_cons_bams",Annot_GR,"SVM_RMBase")

ZhenWei10/RbashGEO documentation built on May 28, 2019, 8:22 a.m.