createCoverageMatrix: Create normalized data frame from input coverage bed files...

In aditiqamra/APcalc: Calculate APscore

Description

Create normalized data frame from input coverage bed files The function will read in bed files, coverage column will be specified by user and collate them to make a data matrix and then normalize by the library size. If the library sizes are not provided by then use sum of reads across loci as proxy. Though this is not recommended.

Usage

createCoverageMatrix(inputPath, filePattern, junctionReads, junctionType,
  promoterFile, gencodefile, normalize, librarySizeFile, ...)

Arguments

inputPath	Path to coverage or junction bed files. Assumptions for coverage bed file - 1st 3 columns are the loci of interest (chr start stop) and the last column is the coverage readcount
filePattern	character string or regular expression to search inputPath to get all coverage files
junctionReads	logical flag specifying whether junction reads are to be calculated OR not
junctionType	character type of the junction bed file. Either 'tophat' or 'star'
promoterFile	Full path file name of promoter loci - needs to be a bed file if junctionReads flag is equal to TRUE
normalize	logical flag specifying whether normalization by library size should be done or not
librarySizeFile	full path file name with library sizes. Should have two columns 1st should be sample name - same as file name in @param inputPath and the 2nd as the library size. No of rows should be equal to no of coverage files read from @param inputpath

Value

A data.frame object with normalized RNAseq reads in each sample (rows)

Author(s)

Aditi Qamra

Examples

## Not run: 
norm_matrix <- createCoverageMatrix(inputPath="readcount/",
                                   filePattern="coverage_",
                                   junctionReads=FALSE,
                                   junctionType='',
                                   promoterFile='',
                                   normalize=TRUE,
                                   librarySizeFile="libsizes.txt")

norm_matrix <- createCoverageMatrix(inputPath="test/",
                                   filePattern=".junction.bed",
                                   junctionReads=TRUE,
                                   junctionType='tophat',
                                   promoterFile='test/aploci.bed',
                                   normalize=TRUE,
                                   librarySizeFile="libsizes.txt")




## End(Not run)

aditiqamra/APcalc documentation built on Jan. 23, 2020, 4:39 p.m.