Count_from_coldata: A highly compact but easy to use function to count based on...
In ZhenWei10/RbashGEO: GEO raw data processing in bash.

Usage Arguments Details Value See Also Examples

1 2	Count_from_coldata(Coldata, Annot_gr, BAM_dir, title = "test", bin_size = 100)

`Coldata`	a data.frame with 2 collumns neccessarily well defined: 1. a collumn named "SRR_RUN". The entries should be character sting consistant with the name of the bam files (before ".bam"). 2. a collumn named "Lib". The entries should be either "Single" or "Paired"
`Annot_gr`	the single based resolution row GRanges used for count.
`BAM_dir`	the directory of your bam files, the function expect all bam files named by "SRR_RUN.bam".
`title`	the title of the file saved.
`bin_zize`	the width of the bin used for count, default is 100.

Under this version, the function is designed to support the count over many (>100) fastq files with both single and paired end data. If you have only single or paired end data, please use Count_SRRs.

The function will output a SummarizedExperiment object well defined colData and rowRanges., it will be saved under current working directory.

Count_SRRs is good for count under other contexts.

library(RbashGEO)
Annot_GR <- GenomicRanges::reduce( readRDS("hg19_union_gr.rds") ,min.gapwidth=0L)
Coldata_df <- read.csv("ColDesign_Meth.csv")
Count_from_coldata(Coldata_df,Annot_GR,"/home/zhen/bam_Metdb","hg19_union_metdb")