Ranges_count: Map unprocessed or processed reads to genome and count small...

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Map unprocessed or processed reads to genome and count small RNAs by location

Description

Map unprocessed or processed reads to genome and count small RNAs by location

Usage

ranges_count(
  fastas,
  miRNA_ranges,
  genomeIndex,
  linkers = NULL,
  length_max = NULL,
  length_min = NULL,
  mode = NULL,
  maxMismatches = 0,
  threads = 1,
  report_k = NULL,
  keep_all = NULL,
  soft_clip = NULL,
  additional_Args = "--score-min C,0,0",
  seedSubString = 18,
  overwrite = FALSE,
  bpparam = NULL,
  verbose = FALSE
)

Arguments

fastas	path to FASTA files to process.
miRNA_ranges	BED file containing annotated miRNA or other small RNA genomic ranges.
genomeIndex	path to genome index.
linkers	contaminating sequences to remove, default is NULL, set to character string to specify.
length_max	maximum length required during fasta processing, default is NULL, set to integer to specify.
length_min	minimum length required during fasta processing, default is NULL, set to integer to specify.
mode	mapping mode, default is NULL to allow custom mapping with default arguments set below (0 mismatches in seed alignment, seed substring length 18, disallow alignments with mismatches); see bowtie_align for other mapping modes.
maxMismatches	max mismatches in seed alignment (default is 0).
threads	number of threads to use (default is 1).
report_k	number of alignments to report, default is NULL (the best alignment is reported), set to integer to specify.
keep_all	set to TRUE to report all alignments, default is NULL (the best alignment is reported).
soft_clip	set to TRUE to allow soft clipping, default is no soft clipping.
additional_Args	any additional mapping arguments, default is "–score-min C,0,0" to disallow alignments with mismatches; run "Rbowtie2::bowtie2_usage()" to see all options; please note that due to a Rbowtie2 bug, the "–no-1mm-upfront" is not available.
seedSubString	length of seed substrings (default is 18).
overwrite	overwrite existing output files, TRUE or FALSE (default).
bpparam	TRUE or FALSE (default)
verbose	print messages, TRUE or FALSE (default).

Value

path to count matrix.

Author(s)

Kathryn Rozen-Gagnon

Examples

testFastq <- system.file("extdata/SRR1742056.fastq.gz",package="CLIPflexR")

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.