projectOntoMGS: projectOntoMGS

In eprifti/momr: Mining Metaomics Data (MetaOMineR)

projectOntoMGS

Description

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

Usage

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

eprifti/momr documentation built on Dec. 11, 2024, 3:06 p.m.