parse_raw_seq: Parse generic

In PoonLab/highlineR: A Novel Visualization Tool to Assess Diversity in NGS Data

Description

Parses the NGS file specified by the path variable of Data objects.

Usage

parse_raw_seq(x, ...)

## S3 method for class 'session'
parse_raw_seq(x, encoding = "sanger", ...)

## S3 method for class 'fasta'
parse_raw_seq(x, encoding = NULL, ...)

## S3 method for class 'fastq'
parse_raw_seq(x, encoding = "sanger", ...)

## S3 method for class 'csv'
parse_raw_seq(x, encoding = NULL, ...)

## Default S3 method:
parse_raw_seq(x, ...)

Arguments

x	Data object or session object containing Data objects to parse.
encoding	A character string representing the quality score encoding of FASTQ files. Options: "Sanger", "Solexa", "Illumina1.3", "Illumina1.5". "Illumina1.8".

Value

Parses Data objects by populating the object's raw_seq list with (header, sequence, [quality scores]) lists.

Methods (by class)

• session: Parse all Data objects in session objects.

• fasta: Parse Data objects of FASTA NGS files.

• fastq: Parse Data objects of FASTQ NGS files.

• csv: Parse Data objects of custom, csv, NGS files.

• default: default.

PoonLab/highlineR documentation built on Aug. 2, 2019, 4:32 p.m.