seastar2counts: Convert seastar output to count data
In armbrustlab/manta: Microbial Assemblage Normalized Transcript Analysis

Description Usage Arguments Value See Also Examples

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

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

`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

a named count matrix or vector

nerge, merge

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)