bc_seq_filter {CellBarcode} | R Documentation |
Remove low quality sequences by base-pair quality, sequence length or unknown base "N".
bc_seq_filter( x, min_average_quality = 30, min_read_length = 0, N_threshold = 0, sample_name = "" ) ## S4 method for signature 'ShortReadQ' bc_seq_filter( x, min_average_quality = 30, min_read_length = 0, N_threshold = 0 ) ## S4 method for signature 'DNAStringSet' bc_seq_filter(x, min_read_length = 0, N_threshold = 0) ## S4 method for signature 'data.frame' bc_seq_filter(x, min_read_length = 0, N_threshold = 0) ## S4 method for signature 'character' bc_seq_filter( x, min_average_quality = 30, min_read_length = 0, N_threshold = 0, sample_name = basename(x) ) ## S4 method for signature 'integer' bc_seq_filter(x, min_read_length = 0, N_threshold = 0) ## S4 method for signature 'list' bc_seq_filter( x, min_average_quality = 30, min_read_length = 0, N_threshold = 0, sample_name = names(x) )
x |
A single or a list of Fastq file, |
min_average_quality |
A numeric or a vector of numeric, specifying the threshold of the minimum average base quality of a sequence to be kept. |
min_read_length |
A single or a vector of integer, specifying the sequence length threshold. |
N_threshold |
A integer or a vector of integer, specifying the maximum
|
sample_name |
A string vector, specifying the sample name in the output. |
A ShortReadQ or DNAStringSet object with sequences passed the filters.
library(ShortRead) fq_file <- system.file("extdata", "simple.fq", package="CellBarcode") # apply filter to fastq files bc_seq_filter(fq_file) # read in fastq files to get ShortReadQ object sr <- readFastq(fq_file[1]) # apply sequencing quality filter to ShortReadQ bc_seq_filter(sr) # get DNAStringSet object ds <- sread(sr) # apply sequencing quality filter to DNAStringSet bc_seq_filter(ds) ###