Count_from_coldata: A highly compact but easy to use function to count based on...

Usage Arguments Details Value See Also Examples

Usage

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

Arguments

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.

Details

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.

Value

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

See Also

Count_SRRs is good for count under other contexts.

Examples

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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")

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