The program removes the sequences with a quality lower the 'minq' threshold

qmean_filter(input, minq, q_format = NULL, check.encod = TRUE)

Arguments

input

ShortReadQ object

minq

Quality threshold

q_format

Quality format used for the file, as returned by check.encoding

check.encod

Check the encoding of the sequence? This argument is incompatible with q_format

Value

Filtered ShortReadQ object

Examples

require(ShortRead) set.seed(10) # create 6 sequences of width 20 input <- random_seq(30, 20) # create qualities of width 20 ## high quality (15 sequences) set.seed(10) my_qual <- random_qual(c(30,40), slength = 15, seed = 10, encod = 'Sanger')
#> Error in random_qual(c(30, 40), slength = 15, seed = 10, encod = "Sanger"): unused argument (seed = 10)
## low quality (15 sequences) set.seed(10) my_qual_2 <- random_qual(c(5,30), slength = 15, seed = 10, encod = 'Sanger')
#> Error in random_qual(c(5, 30), slength = 15, seed = 10, encod = "Sanger"): unused argument (seed = 10)
# concatenate vectors input_q<- c(my_qual, my_qual_2)
#> Error in eval(expr, envir, enclos): objeto 'my_qual' no encontrado
# create names input_names <- seq_names(30) # create ShortReadQ object my_read <- ShortReadQ(sread = input, quality = input_q, id = input_names)
#> Error in ShortReadQ(sread = input, quality = input_q, id = input_names): objeto 'input_q' no encontrado
# watch the average qualities alphabetScore(my_read) / width(my_read)
#> Error in alphabetScore(my_read): objeto 'my_read' no encontrado
# apply the filter filtered <- qmean_filter(my_read, minq = 30)
#> Error in sread(input): objeto 'my_read' no encontrado
# watch the average qualities alphabetScore(my_read) / width(my_read)
#> Error in alphabetScore(my_read): objeto 'my_read' no encontrado
# watch the filtered sequences sread(filtered)
#> Error in sread(filtered): objeto 'filtered' no encontrado