mergeCrisprSets {CrispRVariants} | R Documentation

## Merge two CrisprSets

### Description

Merge two CrisprSet objects sharing a reference and target location

### Usage

    mergeCrisprSets(x, y, ...)

    ## S4 method for signature 'CrisprSet,CrisprSet'
    mergeCrisprSets(x, y, ..., x.samples = NULL,
      y.samples = NULL, names = NULL, order = NULL)

### Arguments

`x` | A CrisprSet object
`y` | A second CrisprSet object
`...` | extra arguments
`x.samples` | A subset of column names or indices to keep from CrispRSet x (Default: NULL, i.e. keep all)
`y.samples` | A subset of column names or indices to keep from CrispRSet y (Default: NULL, i.e. keep all)
`names` | New names for the merged CrisprSet object (Default: NULL)
`order` | A list of sample names, matching the names in x and y, specifying the order of the samples in the new CrisprSet. (Not implemented yet)

### Value

A merged CrisprSet object

### Author(s)

Helen Lindsay

### Examples

    # Load the metadata table
    md_fname <- system.file("extdata", "gol_F1_metadata_small.txt", package = "CrispRVariants")
    md <- read.table(md_fname, sep = "\t", stringsAsFactors = FALSE)

    # Get bam filenames and their full paths
    bam_fnames <- sapply(md$bam.filename, function(fn){
     system.file("extdata", fn, package = "CrispRVariants")})

    reference <- Biostrings::DNAString("GGTCTCTCGCAGGATGTTGCTGG")
    gd <- GenomicRanges::GRanges("18", IRanges::IRanges(4647377, 4647399),
          strand = "+")

    crispr_set1 <- readsToTarget(bam_fnames[c(1:4)], target = gd,
          reference = reference, names = md$experiment.name[1:4], target.loc = 17)
    crispr_set2 <- readsToTarget(bam_fnames[c(5:8)], target = gd,
          reference = reference, names = md$experiment.name[5:8], target.loc = 17)
    mergeCrisprSets(crispr_set1,crispr_set2)

[Package CrispRVariants version 1.12.0 Index]