mergeStrandseqFiles: Merge Strand-seq libraries

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Merge Strand-seq libraries

Description

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

Usage

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 getChromInfoFromUCSC 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 April 18, 2023, 4:20 a.m.