tx_load_bam | R Documentation |
Reads a file in BAM format by blocks of lines equal to a yield size, either automatically calculated or specified by the user, and loads it as a GenomicAlignments object.
tx_load_bam(
file,
pairedEnd,
yieldSize = 1e+05,
scanFlag = "default",
loadSeq = FALSE,
strandMode = 1,
loadSecondaryAligns = NA,
verbose = TRUE
)
file |
character. Path to the file to read |
pairedEnd |
logical. Set to FALSE if reads in BAM file are single-end, set to TRUE if reads are paired-end. |
yieldSize |
numeric. Number of reads to be processed at a time |
scanFlag |
integer. Flag used to filter reads. Built with
the |
loadSeq |
logical. Set to TRUE for loading the sequences contained in the BAM file |
strandMode |
numeric.
More info: |
loadSecondaryAligns |
logical. Set to FALSE to discard alignments labeled in the BAM file as secondary and load only primary alignments, set to TRUE to load only secondary alignments, leave as NA to load both primary and secondary alignments. |
verbose |
logical. Set to FALSE to show less information. |
GRanges
# Loading in-package BAM file
bamFile <- system.file("extdata", "example_hg19.bam", package = "txtools")
hg19_bam <- tx_load_bam(bamFile, pairedEnd = TRUE, loadSeq = TRUE, verbose = TRUE)
summary(hg19_bam)
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