| simpleLibs {ORFik} | R Documentation |
An .obed file containing chromosome, start, stop, strand, readWidth and number of duplicate reads. A bed file with 2 score columns Gives a massive speedup when cigar strings are not needed.
simpleLibs( df, out.dir = paste0(dirname(df$filepath[1]), "/bedo/"), addScoreColumn = TRUE, addSizeColumn = TRUE, must.overlap = NULL )
df |
an ORFik |
out.dir |
optional output directory, default: dirname(df$filepath[1]), if it is NULL, it will just reassign R objects to simplified libraries. |
addScoreColumn |
logical (FALSE), if TRUE, add a score column that sums up the hits per unique range This will make each read unique, so that each read is 1 time, and score column gives the number of hits. A useful compression. If addSizeColumn is FALSE, it will not differentiate between reads with same start and stop, but different length. |
addSizeColumn |
logical (FALSE), if TRUE, add a size column that for each read, that gives original width of read. Useful if you need original read lengths. This takes care of soft clips etc. |
must.overlap |
default (NULL), else a GRanges / GRangesList object, so only reads that overlap (must.overlap) are kept. This is useful when you only need the reads over transcript annotation or subset etc. |
NULL (saves files to disc or R .GlobalEnv)