mergeCrisprSets {CrispRVariants} | R Documentation |
Merge two CrisprSet objects sharing a reference and target location
mergeCrisprSets(x, y, ...) ## S4 method for signature 'CrisprSet,CrisprSet' mergeCrisprSets(x, y, ..., x.samples = NULL, y.samples = NULL, names = NULL, order = NULL)
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) |
A merged CrisprSet object
Helen Lindsay
# 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)