complex_filter.Rd
The program removes low complexity sequences, computing the entropy with the observed frequency of dinucleotides.
complex_filter(input, threshold = 0.5, referenceEntropy = 3.908135)
input |
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threshold | A threshold value computed as the relation of the H of the sequences and the reference H. Default is 0.5 |
referenceEntropy | Reference entropy. By default, the program uses a value of 3.908, that corresponds to the entropy of the human genome in bits |
Filtered ShortReadQ
object
require('Biostrings') require('ShortRead') # create sequences of different width set.seed(10) input <- lapply(c(0, 6, 10, 16, 20, 26, 30, 36, 40), function(x) random_seq(1, x)) # create repetitive 'CG' sequences with length adequante # for a total length: # input + CG = 40 CG <- lapply(c(20, 17, 15, 12, 10, 7, 5, 2, 0), function(x) paste(rep('CG', x), collapse = '')) # concatenate input and CG input <- mapply('paste', input, CG, sep = '') input <- DNAStringSet(input) # plot relative entropy (E, Shannon 1948) freq <- dinucleotideFrequency(input) freq <- freq /rowSums(freq) H <- -rowSums(freq * log2(freq), na.rm = TRUE) H_max <- 3.908135 # max entropy plot(H/H_max, type='b', xlab = 'Sequence', ylab= 'E')# create qualities of width 40 input_q <- random_qual(c(30,40), slength = 9, swidth = 40, seed = 10, encod = 'Sanger')#> Error in random_qual(c(30, 40), slength = 9, swidth = 40, seed = 10, encod = "Sanger"): unused argument (seed = 10)# create names input_names <- seq_names(9) # 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# apply the filter filtered <- complex_filter(my_read)#> Error in sread(input): objeto 'my_read' no encontrado#> Error in sread(filtered): objeto 'filtered' no encontrado