orfFrameDistributions {ORFik} | R Documentation |
Per library: get coverage over CDS per frame per readlength Return as data.datable with information and best frame found. Can be used to automize re-shifting of read lengths (find read lengths where frame 0 is not the best frame over the entire cds)
orfFrameDistributions( df, type = "pshifted", weight = "score", BPPARAM = BiocParallel::bpparam() )
df |
an ORFik |
type |
type of library loaded, default pshifted, warning if not pshifted might crash if too many read lengths! |
weight |
which column in reads describe duplicates, default "score". |
BPPARAM |
how many cores/threads to use? default: bpparam().
To see number of threads used, do |
data.table with columns: fraction (library) frame (0, 1, 2) score (coverage) length (read length) percent (coverage percentage of library) percent_length (coverage percentage of library and length) best_frame (TRUE/FALSE, is this the best frame per length)
df <- ORFik.template.experiment()[3,] dt <- orfFrameDistributions(df, BPPARAM = BiocParallel::SerialParam()) ## Check that frame 0 is best frame for all all(dt[frame == 0,]$best_frame)