Removes a set of sequences

seq_filter(input, rm.seq)

Arguments

input

ShortReadQ object

rm.seq

Ccharacter vector with sequences to remove

Value

Filtered ShortReadQ object

Examples

require(ShortRead) set.seed(10) input <- random_length(30, 3:7) rm.seq = c('TGGTC', 'CGGT', 'GTTCT', 'ATA') # verify that some sequences match match_before <- unlist(lapply(rm.seq, function(x) grep(x, as.character(sread(input))))) filtered <- seq_filter(input,rm.seq = rm.seq) # verify that matching sequences were removed match_after <- unlist(lapply(rm.seq, function(x) grep(x, as.character(sread(filtered)))))