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)

Arguments

input

ShortReadQ object

rm.min

Threshold value for the minimun number of bases

rm.max

Threshold value for the maximum number of bases

Value

Filtered ShortReadQ object

Examples

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 length < 10 or length > 80 filtered <- length_filter(input, rm.min = 10, rm.max = 80) # look at the filtered sequences sread(filtered)
#> A DNAStringSet instance of length 73 #> width seq #> [1] 74 GTACTTCCACAGTCAACCCGCCGACTTGGAGAA...CCGGGCGGTTATTCCCCTAGTGATCTTACTAAG #> [2] 76 ATTTGCAATACCTAAGCGAAGTGACAGATATGT...TCCAGGCAAGTGCGCGGACATCAATTACCACAC #> [3] 55 AATTAAATATGACTCGCGTATCGCACGTGACCCCTTTGATGCGGACTACCATTCA #> [4] 72 CAGCTCAAGAAATTGGAATTTGTGCTGGTAAGG...CTGAACGCTCCGTCTCTCTCAATTAAGACCGTT #> [5] 54 ATCCGCCGTTAAGACATTCCACGCGGCAGAGCTTGAGCAATCAGTGACGCCGGG #> ... ... ... #> [69] 77 TGGCCACGCGCCCTATATTCCGCGCAGTTTCAT...ACCGCTGGTTTATTTCTAATTGGTTTCCCACTG #> [70] 78 TCGGCTGTTATACCGGGTTGCCCTTCCATGAGA...AAAAAAGTCAAAACGTTCGGCCGCTGCACTCAT #> [71] 34 TCGTATACAGCGAGTGTCTAACTTGAAGGTATTA #> [72] 64 GATCTGAACTGCAGTTGACTGCCTCATTAACGCGTTACGGACTACTGGGGGAAAGGTGGCTACC #> [73] 63 CAGGGAGGCCATGTCCTCGGGAAGAGATAGAGCGGGACGGCTGCCTAGTGGCAGTACCCGCTC