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

In 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

• meta a metadate matrix

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(meta=meta, label="label", case = "cancer")
siamcat <- siamcat(feat=feat, label=label, meta=meta)

SIAMCAT documentation built on Nov. 8, 2020, 5:14 p.m.