tx_makeDT_coverage | R Documentation |
This function constructs a data.table that contains coverage metrics per nucleotide for all transcripts with corresponding GRanges in its first argument 'x':
cov = Insert coverage
start_5p = read-start counts
end_3p = read-end counts
tx_makeDT_coverage(x, geneAnnot, genome = NULL, fullDT = FALSE, nCores = 1)
x |
CompressedGRangesList. Genomic Ranges list containing genomic
alignments data by gene. Constructed via the |
geneAnnot |
GRanges. Gene annotation as loaded by |
genome |
list. The full reference genome sequences, as loaded by
|
fullDT |
logical. Set to TRUE if it is desired to output a data.table with all genes and in the same order as 'geneAnnot' object. |
nCores |
integer. Number of cores to run the function with. Multicore capability not available in Windows OS. |
data.table
M.A. Garcia-Campos
Other makeDT functions:
tx_makeDT_covNucFreq()
,
tx_makeDT_nucFreq()
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.