Splits autosomes (chr1-chr22) into fixed-size segments and writes a SAF file
compatible with Rsubread::featureCounts.
Usage
cacti_s_create_segments(
file_saf_out,
genome = c("hg19", "hg38"),
segment_size = "5kb"
)
Arguments
- file_saf_out
Output path for the SAF file.
- genome
Genome build to use: "hg19" (default) or "hg38".
- segment_size
Character like "5kb" or numeric bp (e.g. 5000).
Default is "5kb".
Value
Invisibly returns the segment data frame. Writes file_saf_out to disk.
Details
This function uses built-in chromosome sizes for hg19 or hg38.
It strictly filters the genome to include only chromosomes named "chr1" through "chr22".
Sex chromosomes (chrX, chrY) and mitochondrial DNA (chrM) are excluded.
Examples
if (FALSE) { # \dontrun{
# Create 5kb segments for hg19 (default)
cacti_s_create_segments("inst/extdata/test_results/test_segments.saf")
# Create 1kb segments for hg38
cacti_s_create_segments("inst/extdata/test_results/test_segments.saf", genome = "hg38", segment_size = "1kb")
} # }