qmean_filter {FastqCleaner} | R Documentation |
The program removes the sequences with a quality lower the 'minq' threshold
qmean_filter(input, minq, q_format = NULL, check.encod = TRUE)
input |
|
minq |
Quality threshold |
q_format |
Quality format used for the file, as returned by check.encoding |
check.encod |
Check the encoding of the sequence? This argument is incompatible with q_format |
Filtered ShortReadQ
object
Leandro Roser learoser@gmail.com
require(ShortRead) set.seed(10) # create 30 sequences of width 20 input <- random_seq(30, 20) # create qualities of width 20 ## high quality (15 sequences) set.seed(10) my_qual <- random_qual(c(30,40), slength = 15, swidth = 20, encod = 'Sanger') ## low quality (15 sequences) set.seed(10) my_qual_2 <- random_qual(c(5,30), slength = 15, swidth = 20, encod = 'Sanger') # concatenate vectors input_q<- c(my_qual, my_qual_2) # create names input_names <- seq_names(30) # create ShortReadQ object my_read <- ShortReadQ(sread = input, quality = input_q, id = input_names) # watch the average qualities alphabetScore(my_read) / width(my_read) # apply the filter filtered <- qmean_filter(my_read, minq = 30) # watch the average qualities alphabetScore(my_read) / width(my_read) # watch the filtered sequences sread(filtered)