Filter sequences by their average quality — qmean_filter • FastqCleaner
Description: The program removes the sequences with a quality lower the 'minq' threshold

# Filter sequences by their average quality

`qmean_filter.Rd`

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 30 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, swidth = 20,
                           encod = 'Sanger')
    ## low quality (15 sequences)
    set.seed(10)
    my_qual_2 <-   random_qual(c(5,30), slength = 15, swidth = 20,
                               encod = 'Sanger')

    # concatenate vectors
    input_q<- c(my_qual, my_qual_2)

    # create names
    input_names <- seq_names(30)

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

    # watch the average qualities
    alphabetScore(my_read) / width(my_read)#>  [1] 34.95 34.65 36.55 34.80 35.20 35.35 34.65 34.20 34.45 35.05 34.80 34.70
    #> [13] 34.40 34.80 35.85 15.95 16.55 19.65 16.85 16.65 18.20 16.80 18.00 14.85
    #> [25] 18.90 17.00 16.65 16.15 16.80 20.35
    # apply the filter
    filtered <- qmean_filter(my_read, minq = 30)

    # watch the average qualities
    alphabetScore(my_read) / width(my_read)#>  [1] 34.95 34.65 36.55 34.80 35.20 35.35 34.65 34.20 34.45 35.05 34.80 34.70
    #> [13] 34.40 34.80 35.85 15.95 16.55 19.65 16.85 16.65 18.20 16.80 18.00 14.85
    #> [25] 18.90 17.00 16.65 16.15 16.80 20.35

    # watch the filtered sequences
    sread(filtered)#>   A DNAStringSet instance of length 15
    #>      width seq
    #>  [1]    20 TGGTCCGGTGTTCTGGCGGA
    #>  [2]    20 ATAGGTACAGTCCAGTAATT
    #>  [3]    20 GCCTCCCGCAGACGCTGGGT
    #>  [4]    20 CCGGAATGCCCTTTCTGAGC
    #>  [5]    20 AGCTCCAGCCGTTTGACTTC
    #>  ...   ... ...
    #> [11]    20 CTTACTAAGATTTGCAATAC
    #> [12]    20 CTAAGCGAAGTGACAGATAT
    #> [13]    20 GTTCGTCATTCATCCAGGCA
    #> [14]    20 AGTGCGCGGACATCAATTAC
    #> [15]    20 CACACAATTAAATATGACTC