read.lefse: read an input file in a LEfSe input format

In KonradZych/SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes

Description

This reads an input file in a LEfSe input format

Usage

read.lefse(filename = "data.txt", rows.meta = 1, row.samples = 2)

Arguments

filename	name of the input file in a LEfSe input format
rows.meta	specifies in which rows medata variables are stored
row.samples	specifies in which row sample names are stored

Value

a list with two elements:

• feat a features matrix (just as returned by read.features function

• meta a metadate matrix (just as returned by read.meta function

Examples

fn.in.lefse<- system.file("extdata",
"LEfSe_crc_zeller_msb_mocat_specI.tsv",package = "SIAMCAT")
meta.and.features <- read.lefse(fn.in.lefse, rows.meta = 1:6, 
row.samples = 7)
meta <- meta.and.features$meta
feat <- meta.and.features$feat
label <- create.label.from.metadata(meta, "label", case = "cancer")
siamcat <- siamcat(feat, label, meta)

KonradZych/SIAMCAT documentation built on May 17, 2019, 6:20 p.m.