stats4trim {Rqc} | R Documentation |
This function estimates how many reads would be lost if the sequences are filtered by a minimum read mean quality value. Also this function estimates what is the minimum read mean quality value for filtering and lose max percentage defined.
stats4trim(rqcResultSet, qmin, pmax)
rqcResultSet |
list of |
qmin |
Minimum read mean quality value (bewteen 0 and 41). |
pmax |
Maximum percentage of reads permitted been lost during trimming step. |
A data frame containg estimated minimum quality and maximum percentage for each input file.
Welliton Souza
checkpoint("Rqc", path=system.file(package="Rqc", "extdata"), { folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147") files <- list.files(full.names=TRUE, path=folder) rqcResultSet <- rqcQA(files, pair=c(1,1), workers=1) }, keep="rqcResultSet") stats4trim(rqcResultSet, qmin=20) stats4trim(rqcResultSet, pmax=10)