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

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

Kathryn Rozen-Gagnon

Examples

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