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Summarized Coverage data.table

tx_makeDT_coverage.Rd

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

Usage

tx_makeDT_coverage(x, geneAnnot, genome = NULL, fullDT = FALSE, nCores = 1)

Arguments

x

CompressedGRangesList. Genomic Ranges list containing genomic alignments data by gene. Constructed via the tx_reads function.

geneAnnot

GRanges. Gene annotation as loaded by tx_load_bed()

genome

list. The full reference genome sequences, as loaded by tx_load_genome() or prepackaged by BSgenome, see ?BSgenome::available.genomes

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.

Value

data.table

See also

Other makeDT functions: tx_makeDT_covNucFreq(), tx_makeDT_nucFreq()

Author

M.A. Garcia-Campos