normfact2absTMM {manta} | R Documentation

## Convert a count or alignment table into a MANTA object

### 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

    normfact2absTMM(x, pair, f=nv(x$samples, 'norm.factors'), sums=colSums(x$counts))

### Arguments

`x` | The manta object (can be NULL if f and sums are specified independently).
`pair` | A named vector indicating the condition names and the corresponding the reference or observation status of each.
`f` | The Normalization factors. By default uses the norm.factors column of the sample dataframe in x.
`sums` | The column sums of the counts. By default uses the column sums of the x$counts table.

### Value

a scalar normalization factor

### See Also

manta, mantaMethod

### Examples

    conditions <- caroline::nv(factor(x=1:2, labels=c('ambient','plusFe')) ,c('ref','obs'))
    manta.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.Rdata", package="manta")
    load(manta.path)

    x$mm <- normfact2absTMM(x=x, pair=conditions)

[Package manta version 1.26.0 Index]