calc_over_rep_seq {qckitfastq}R Documentation

Calculate sequece counts for each unique sequence and create a table with unique sequences and corresponding counts

Description

Calculate sequece counts for each unique sequence and create a table with unique sequences and corresponding counts

Usage

calc_over_rep_seq(infile, min_size = 5L, buffer_size = 1000000L)

Arguments

infile

A string giving the path for the fastqfile

min_size

An int for thhresholding over representation

buffer_size

An int for the number of lines to keep in memory

Value

calculate overrepresented sequence count

Examples

infile <- system.file("extdata", "10^5_reads_test.fq.gz", package = "qckitfastq")
calc_over_rep_seq(infile)[seq_len(5)]

[Package qckitfastq version 1.0.1 Index]