| n_filter {FastqCleaner} | R Documentation |
This program is a wrapper to
nFilter.
It removes the sequences with a number of N's above
a threshold value 'rm.N'.
All the sequences with a number of N > rm.N (N >= rm.N) will be removed
n_filter(input, rm.N)
input |
|
rm.N |
Threshold value of N's to remove a sequence from the output (sequences with number of Ns > threshold are removed) For example, if rm.N is 3, all the sequences with a number of Ns > 3 (Ns >= 4) will be removed |
Filtered ShortReadQ
object
Leandro Roser learoser@gmail.com
require('Biostrings')
require('ShortRead')
# create 6 sequences of width 20
set.seed(10)
input <- random_seq(50, 20)
# inject N's
set.seed(10)
input <- inject_letter_random(input, how_many_seqs = 1:30,
how_many = 1:10)
input <- DNAStringSet(input)
# watch the N's frequency
hist(letterFrequency(input, 'N'), breaks = 0:10,
main = 'Ns Frequency', xlab = '# Ns')
# create qualities of width 20
set.seed(10)
input_q <- random_qual(50, 20)
# create names
input_names <- seq_names(50)
# create ShortReadQ object
my_read <- ShortReadQ(sread = input, quality = input_q, id = input_names)
# apply the filter
filtered <- n_filter(my_read, rm.N = 3)
# watch the filtered sequences
sread(filtered)
# watch the N's frequency
hist(letterFrequency(sread(filtered), 'N'),
main = 'Ns distribution', xlab = '')