compress: Compress generic

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

Description

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

read_sample samples N number of sequences from the compressed environment M times.

resample resamples Data objects without re-compressing.

Usage

compress(x, N, M, unique, force)

## S3 method for class 'session'
compress(x, N = 500, M = 10, unique = F,
  force = F)

## S3 method for class 'Data'
compress(x, N = 500, M = 10, unique = F, force = F)

## Default S3 method:
compress(x, N, M, unique, force)

read_sample(x, N, M)

resample(x, N, M)

## S3 method for class 'session'
resample(x, N = 500, M = 10)

## S3 method for class 'Data'
resample(x, N = 500, M = 10)

Arguments

x	Data object or session object containing Data objects to compress.
N	Integer expected number of reads.
M	Integer number of random samples to select from dataset for read averaging.
unique	A logical value specifying whether the NGS data file contains unique sequences. If True, then it is assumed that read counts are present in sequence labels. If False, then read counts are inferred from the number of distinct instances of sequences in the file.
force	A logical value specifying if previously imported file should be overwritten and re-imported.

Value

Compresses Data objects by populating the object's compressed environment with (sequence: abundance) key:value pairs.

read_sample samples N number of sequences from the compressed evironment M times and stores the average result in the Data object's sample environment.

resample resamples Data objects by overwriting the object's sample environment with (sequence: abundance) key:value pairs without re-compressing.

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