mergeStrandseqFiles: Merge Strand-seq libraries

Description Usage Arguments Value

View source: R/blacklist.R

Description

Merge strand libraries to generate a high-coverage Strand-seq library.

Usage

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mergeStrandseqFiles(files, assembly, chromosomes = NULL,
  pairedEndReads = FALSE, min.mapq = 10, remove.duplicate.reads = TRUE,
  max.fragment.width = 1000)

Arguments

files

A character vector with files with aligned reads.

assembly

Please see fetchExtendedChromInfoFromUCSC for available assemblies. Only necessary when importing BED files. BAM files are handled automatically. Alternatively a data.frame with columns 'chromosome' and 'length'.

chromosomes

If only a subset of the chromosomes should be imported, specify them here.

pairedEndReads

Set to TRUE if you have paired-end reads in your BAM files (not implemented for BED files).

min.mapq

Minimum mapping quality when importing from BAM files. Set min.mapq=NA to keep all reads.

remove.duplicate.reads

A logical indicating whether or not duplicate reads should be removed.

max.fragment.width

Maximum allowed fragment length. This is to filter out erroneously wrong fragments due to mapping errors of paired end reads.

Value

A GRanges-class object with reads.


ataudt/aneufinder documentation built on Nov. 21, 2018, 10:10 a.m.