adapter_filter {FastqCleaner} | R Documentation

## Remove full and partial adapters from a ShortReadQ object

### Description

This program can remove adapters and partial adapters from 3' and 5', using the functions `trimLRPatterns` The program extends the methodology of the `trimLRPatterns` function of Biostrings, being also capable of removing adapters present within reads and with other additional otpions (e.g., threshold of minimum number of bases for trimming). For a given position in the read, the two Biostrings functions return TRUE when a match is present between a substring of the read and the adapter. As `trimLRPatterns` , adapter_filter also selects region and goes up to the end of the sequence in the corresponding flank as the best match. The default error rate is 0.2. If several valid matches are found, the function removes the largest subsequence. Adapters can be anchored or not. When indels are allowed, the second method uses the 'edit distance' between the subsequences and the adapter

### Usage

    adapter_filter(input, Lpattern = "", Rpattern = "", rc.L = FALSE,
      rc.R = FALSE, first = c("R", "L"), with_indels = FALSE,
      error_rate = 0.2, anchored = TRUE, fixed = "subject",
      remove_zero = TRUE, checks = TRUE, min_match_flank = 3L, ...)

### Arguments

`input` | `ShortReadQ` object
`Lpattern` | 5' pattern (character or `DNAString` object)
`Rpattern` | 3' pattern (character or `DNAString` object)
`rc.L` | Reverse complement Lpattern? default FALSE
`rc.R` | Reverse complement Rpatter? default FALSE
`first` | trim first right('R') or left ('L') side of sequences when both Lpattern and Rpattern are passed
`with_indels` | Allow indels? This feature is available only when the error_rate is not null
`error_rate` | Error rate (value in the range [0, 1] The error rate is the proportion of mismatches allowed between the adapter and the aligned portion of the subject. For a given adapter A, the number of allowed mismatches between each subsequence s of A and the subject is computed as: error_rate * L_s, where L_s is the length of the subsequence s
`anchored` | Adapter or partial adapter within sequence (anchored = FALSE, default) or only in 3' and 5' terminals? (anchored = TRUE)
`fixed` | Parameter passed to `trimLRPatterns` Default 'subject', ambiguities in the pattern only are interpreted as wildcard. See the argument fixed in `trimLRPatterns`
`remove_zero` | Remove zero-length sequences? Default TRUE
`checks` | Perform checks? Default TRUE
`min_match_flank` | Do not trim in flanks of the subject, if a match has min_match_flank of less length. Default 1L (only trim with >=2 coincidences in a flank match)
`...` | additional parameters passed to `trimLRPatterns`

### Value

Edited `DNAString` or `DNAStringSet` object

Filtered `ShortReadQ` object

### Author(s)

Leandro Roser learoser@gmail.com

### Examples

    require('Biostrings')
    require('ShortRead')

    # create 6 sequences of width 43
    set.seed(10)
    input <- random_seq(6, 43)

    # add adapter in 3'
    adapter <- "ATCGACT"

    input <- paste0(input, as.character(DNAString(adapter)))
    input <- DNAStringSet(input)

    # create qualities of width 50
    set.seed(10)
    input_q <- random_qual(c(30,40), slength = 6, swidth = 50,
    encod = 'Sanger')

    # create names
    input_names <- seq_names(length(input))

    # create ShortReadQ object
    my_read <- ShortReadQ(sread = input, quality = input_q, id = input_names)

    # trim adapter
    filtered <- adapter_filter(my_read, Rpattern = adapter)

    # look at the filtered sequences
    sread(filtered)

[Package FastqCleaner version 1.12.0 Index]