revmap_count: Reverse map small RNAs to processed or unprocessed reads

View source: R/Functions.R

revmap_countR Documentation

Reverse map small RNAs to processed or unprocessed reads

Description

Reverse map small RNAs to processed or unprocessed reads

Usage

revmap_count(
  fastas,
  knownMiRNAs,
  bpparam = NULL,
  verbose = FALSE,
  linkers = NULL,
  length_max = NULL,
  length_min = NULL,
  removedups = TRUE,
  overwrite = FALSE,
  make_index = TRUE
)

Arguments

fastas

path to FASTA files to reverse map.

knownMiRNAs

path to FASTA file containing annotated miRNA or other small RNA sequences.

bpparam

TRUE or FALSE (default).

verbose

print messages, TRUE or FALSE (default).

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.

removedups

remove multiple miRNAs or small RNAs mapping to the same read, TRUE (default) or FALSE. If TRUE, known miRNAs will be prioritized and known miRNA names must be in the format "miR-", "let-", "bantam-", "iab-".

overwrite

overwrite existing output files, TRUE or FALSE (default).

make_index

make bowtie2 index of reads, TRUE (default) or FALSE. If set to FALSE, indices should be in the same directory as reads.

Value

path to BEDs where small RNAs mapped to reads.

Author(s)

Kathryn Rozen-Gagnon

Examples

testFastq <- system.file("extdata/SRR1742056.fastq.gz",package="CLIPflexR")
FqFile <- decompress(testFastq,overwrite = TRUE)
FaFile <- fastx_qtoa(FqFile)
FaFile_clip <- fastx_clipper(FaFile, writelog = FALSE)
testMiRNA <- system.file("extdata/hsa_mature.fa",package="CLIPflexR")
revmap <- revmap_count(FaFile_clip, testMiRNA, 
linkers="GGACGATGC", length_min=18, length_max=30, overwrite=TRUE)

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