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 1.8.0 Index]