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.
1 2 3 4 | 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")
|
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