mergeStrandseqFiles {AneuFinder} | R Documentation

## 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 `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.

[Package AneuFinder version 1.8.0 Index]