readPathoscopeData: Reads the data from PathoScope reports and returns a list of...

In PathoStat: PathoStat Statistical Microbiome Analysis Package

Description

Reads the data from PathoScope reports and returns a list of final guess relative abundance and count data

Usage

readPathoscopeData(input_dir = ".",
  pathoreport_file_suffix = "-sam-report.tsv", use.input.files = FALSE,
  input.files.path.vec = NULL, input.files.name.vec = NULL)

Arguments

input_dir	Directory where the tsv files from PathoScope are located
pathoreport_file_suffix	PathoScope report files suffix
use.input.files	whether input dir to pathoscope files or directly pathoscope files
input.files.path.vec	vector of pathoscope file paths
input.files.name.vec	vector of pathoscope file names

Value

List of final guess relative abundance and count data

Examples

example_data_dir <- system.file("example/data", package = "PathoStat")
pathoreport_file_suffix <- "-sam-report.tsv"
datlist <- readPathoscopeData(example_data_dir, pathoreport_file_suffix,
input.files.name.vec = as.character(1:6))

PathoStat documentation built on Nov. 8, 2020, 5:28 p.m.