getSpikeInCounts {BRGenomics} | R Documentation |
Filtering and counting spike-in reads
getSpikeInCounts( dataset.gr, si_pattern = NULL, si_names = NULL, field = "score", sample_names = NULL, expand_ranges = FALSE, ncores = getOption("mc.cores", 2L) ) removeSpikeInReads( dataset.gr, si_pattern = NULL, si_names = NULL, field = "score", ncores = getOption("mc.cores", 2L) ) getSpikeInReads( dataset.gr, si_pattern = NULL, si_names = NULL, field = "score", ncores = getOption("mc.cores", 2L) )
dataset.gr |
A GRanges object or a list of GRanges objects. |
si_pattern |
A regular expression that matches spike-in chromosomes. Can
be used in addition to, or as an alternative to |
si_names |
A character vector giving the names of the spike-in
chromosomes. Can be used in addition to, or as an alternative to
|
field |
The metadata field in |
sample_names |
An optional character vector used to rename the datasets
in |
expand_ranges |
Logical indicating if ranges in |
ncores |
The number of cores to use for computations. |
A dataframe containing total readcounts, experimental (non-spike-in) readcounts, and spike-in readcounts.
Mike DeBerardine
#--------------------------------------------------# # Make list of dummy GRanges #--------------------------------------------------# gr1_rep1 <- GRanges(seqnames = c("chr1", "chr2", "spikechr1", "spikechr2"), ranges = IRanges(start = 1:4, width = 1), strand = "+") gr2_rep2 <- gr2_rep1 <- gr1_rep2 <- gr1_rep1 # set readcounts score(gr1_rep1) <- c(1, 1, 1, 1) # 2 exp + 2 spike = 4 total score(gr2_rep1) <- c(2, 2, 1, 1) # 4 exp + 2 spike = 6 total score(gr1_rep2) <- c(1, 1, 2, 1) # 2 exp + 3 spike = 5 total score(gr2_rep2) <- c(4, 4, 2, 2) # 8 exp + 4 spike = 12 total grl <- list(gr1_rep1, gr2_rep1, gr1_rep2, gr2_rep2) names(grl) <- c("gr1_rep1", "gr2_rep1", "gr1_rep2", "gr2_rep2") grl #--------------------------------------------------# # Count spike-in reads #--------------------------------------------------# # by giving names of all spike-in chromosomes getSpikeInCounts(grl, si_names = c("spikechr1", "spikechr2"), ncores = 1) # or by matching the string/regular expression "spike" in chromosome names getSpikeInCounts(grl, si_pattern = "spike", ncores = 1) #--------------------------------------------------# # Filter out spike-in reads #--------------------------------------------------# removeSpikeInReads(grl, si_pattern = "spike", ncores = 1) #--------------------------------------------------# # Return spike-in reads #--------------------------------------------------# getSpikeInReads(grl, si_pattern = "spike", ncores = 1)