| length_filter {FastqCleaner} | R Documentation |
The program removes from a ShortReadQ object those sequences with a length lower than rm.min or/and higher than rm.max
length_filter(input, rm.min = NA, rm.max = NA)
input |
|
rm.min |
Threshold value for the minimun number of bases |
rm.max |
Threshold value for the maximum number of bases |
Filtered ShortReadQ
object
Leandro Roser learoser@gmail.com
require('Biostrings')
require('ShortRead')
# create ShortReadQ object width widths between 1 and 100
set.seed(10)
input <- random_length(100, widths = 1:100)
# apply the filter, removing sequences with 10> length > 80
filtered <- length_filter(input, rm.min = 10, rm.max = 80)
# look at the filtered sequences
sread(filtered)