align.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.tab", package="manta")
a <- read.delim(align.path, stringsAsFactors=FALSE)
x <- align2manta(a, cond.clmn='treatment', agg.clmn='what_def',
gene.clmns=c('what_def','kid','pathway'),
meta.clmns=c('family','genus_sp'))
cts.path <- system.file("extdata","PapaGO-BWA.counts-diatoms.tab", package="manta")
cts <- read.delim(cts.path)
cts.annot.path <- system.file("extdata","PapaGO-BWA.annot-diatoms.tab", package="manta")
cts.annot <- read.delim(cts.annot.path, stringsAsFactors=FALSE)
x <- counts2manta(cts, annotation=cts.annot,
a.merge.clmn='query_seq', agg.clmn='what_def', meta.clmns=c('family','genus_sp'),
gene.clmns=c('what_def','kid','pathway'))
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