R/Functions.R
Ranges_count.RdMap 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
)path to FASTA files to process.
BED file containing annotated miRNA or other small RNA genomic ranges.
path to genome index.
contaminating sequences to remove, default is NULL, set to character string to specify.
maximum length required during fasta processing, default is NULL, set to integer to specify.
minimum length required during fasta processing, default is NULL, set to integer to specify.
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.
max mismatches in seed alignment (default is 0).
number of threads to use (default is 1).
number of alignments to report, default is NULL (the best alignment is reported), set to integer to specify.
set to TRUE to report all alignments, default is NULL (the best alignment is reported).
set to TRUE to allow soft clipping, default is no soft clipping.
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.
length of seed substrings (default is 18).
overwrite existing output files, TRUE or FALSE (default).
TRUE or FALSE (default)
print messages, TRUE or FALSE (default).
path to count matrix.
testFastq <- system.file("extdata/SRR1742056.fastq.gz",package="CLIPflexR")