in2manta: Convert a count or alignment table into a MANTA object

In armbrustlab/manta: Microbial Assemblage Normalized Transcript Analysis

Description

This function converts a table of alignment data (BLAST for example) where each record is a read and each column is some parameter of the blast(s). The function will perform a cross-tabulation of the annotated reads into count data using (at the very least) an aggregation index column and a condition column. Alternatively, the input can be pre-tabulated counts and a corresponding annotation table. The two tableMeta helper functions (called by the x2manta functions) are also documented here.

Usage

align2manta(x, cond.clmn, agg.clmn, gene.clmns, meta.clmns, weight.clmn=NULL, tag.clmn=NULL, ...)
counts2manta(x, annotation, a.merge.clmn, agg.clmn, gene.clmns=NULL, meta.clmns=NULL, ...)
tableMetaSums(x, meta.clmns, cond.clmn=NULL, count.clmns=NULL)
tableMetas(x, agg.clmn, meta.clmns, cond.clmn=NULL, count.clmns=NULL)

Arguments

x	The alignment or counts table.
cond.clmn	A string indicating which column contains the conditions. (only two different levels two allowed)
agg.clmn	A string indicating which column in the annotation table contains the aggregation index.
annotation	An annotation table with genes and/or meta information.
a.merge.clmn	A stringn indicating which column in the annotation table on which to merge. These should correspond to the row names of the counts table.
gene.clmns	A vector of strings indicating which column contains gene annotation information.
meta.clmns	A vector of strings indicating which column contains meta/taxinomic information.
weight.clmn	A string indicating which column contains weighting information.
count.clmns	A string indicating which column in a pre-cross-tabulated meta annotation table contains counts. These counts are multiplied by the result of tableMetas()'s cross-tabulated counts to genereate the meta tables.
tag.clmn	A string indicating which column corresponds to individual read names. Only necessary when a single read has multiple annotation records in the table.
...	additional parameters passed along to manta()

Value

A MANTA object

See Also

manta

Examples

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'))

armbrustlab/manta documentation built on Dec. 17, 2019, 12:06 a.m.