fixed_filter.Rd
The program removes a given number of bases from the 3' or 5' regions of the sequences contained in a ShortReadQ object
fixed_filter(input, trim3 = NA, trim5 = NA)
input |
|
---|---|
trim3 | Number of bases to remove from 3' |
trim5 | Number of bases to remove from 5' |
Filtered ShortReadQ
object
require('Biostrings') require('ShortRead') # create 6 sequences of width 20 set.seed(10) input <- random_seq(6, 20) # create qualities of width 20 set.seed(10) input_q <- random_qual(c(30,40), slength = 6, swidth = 20, encod = 'Sanger') # create names input_names <- seq_names(6) # create ShortReadQ object my_read <- ShortReadQ(sread = input, quality = input_q, id = input_names) # apply the filter filtered3 <- fixed_filter(my_read, trim5 = 5) filtered5 <- fixed_filter(my_read, trim3 = 5) filtered3and5 <- fixed_filter(my_read, trim3 = 10, trim5 = 5) # look at the trimmed sequences sread(filtered3)#> A DNAStringSet instance of length 6 #> width seq #> [1] 15 TGGTCCGGTGTTCTG #> [2] 15 ATAGGTACAGTCCAG #> [3] 15 GCCTCCCGCAGACGC #> [4] 15 CCGGAATGCCCTTTC #> [5] 15 AGCTCCAGCCGTTTG #> [6] 15 GCGGAAAGTGAACTTsread(filtered5)#> A DNAStringSet instance of length 6 #> width seq #> [1] 15 CGGTGTTCTGGCGGA #> [2] 15 TACAGTCCAGTAATT #> [3] 15 CCGCAGACGCTGGGT #> [4] 15 ATGCCCTTTCTGAGC #> [5] 15 CAGCCGTTTGACTTC #> [6] 15 AAGTGAACTTAGATTsread(filtered3and5)#> A DNAStringSet instance of length 6 #> width seq #> [1] 5 TTCTG #> [2] 5 TCCAG #> [3] 5 GACGC #> [4] 5 CTTTC #> [5] 5 GTTTG #> [6] 5 AACTT