projectOntoMGS

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Description

This function takes a list of genes and projects it to a mgs catalogue

Usage

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projectOntoMGS(genebag, list.mgs, res.filt.mode = "size",
  res.filt.threshold = 50, not_projected = TRUE)

Arguments

genebag

: vector of gene_ids

list.mgs

: this is the structured MGS information formatted as a list of geneids each corresponding to an MGS

res.filt.mode

: the filtering method, either 'perc' or 'size', default will be size. perc : genes projected onto mgs are only kept if they exceed a threshold percentage of the mgs size size : genes projected onto mgs are only kept if they exceed a threshold number of genes

res.filt.threshold

: the threshold used to retain an mgs according to the filtering mode, either 'perc' or 'size' if 'perc' : the minimal percentage of genes projected onto mgs (number of genes projected / mgs size) needed to select a mgs if 'size' : the minimal number of genes projected onto mgs

not_projected

: whether a last genebag containing not projected genes is to be added to the list of selected mgs

Details

projectOntoMGS

Value

a list of selected mgs with the geneids according to the projected genes

Author(s)

Edi Prifti & Emmanuelle Le Chatelier

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