seastar2counts: Convert seastar output to count data

In manta: Microbial Assemblage Normalized Transcript Analysis

Description

This function performs a simple merge between two different SEAStAR tables.

Usage

seastar2counts(treat.paths, id.prefix=NA, all=TRUE, uniques=0, ...)

Arguments

treat.paths	a named vector of strings of paths to 2 seastar tabular files.
id.prefix	prefix to use when naming the rownames of the merged table
all	used in the same way as the underlying merge function's all parameter.
uniques	determines the replacement value for genes which are unique to the opposite library.
...	additional paramters passed on to readSeastar

Value

a named count matrix or vector

See Also

nerge, merge

Examples

conditions <- c('ambient','plusFe')
ss.names <- caroline::nv(paste('Pgranii-',conditions,'.seastar', sep=''), conditions)

ss.paths <- caroline::nv(system.file("extdata",ss.names, package="manta"), conditions)

dfm <- seastar2counts(ss.paths)

manta documentation built on Oct. 31, 2019, 3:03 a.m.