buildMgsFinal: buildMgsFinal

In eprifti/momr: Mining Metaomics Data (MetaOMineR)

buildMgsFinal

Description

This function will take a vector of genes (to be transformed into a list of genebags) or a list of genebags and will extract the profiles. Next genes well be ordered by connectivity which is to be computed for each group and the 50 most connected are selected to consitute the marker genes. These will be then used to compute the mean vectors. A final object containing all this information along with taxonomical annotation will be returned

Usage

buildMgsFinal(
  genebag = NULL,
  mgs.cat,
  mgs.taxo,
  profiles,
  conn = TRUE,
  silent = TRUE,
  filt = 10,
  save = FALSE
)

Arguments

genebag	: a vector of genes to be projected onto mgs or a list of genebags, default = NULL.
mgs.cat	: MGS catalogue to be used
mgs.taxo	: taxonomy table for the MGS catalogue
profiles	: the data profile matrix to extract the profiles
conn	: if TRUE the connectivity of a group is to be computed and ordered, default = TRUE.
silent	: print detailled information on progress, default = FALSE.
filt	: filtering based on percentage of prevalence to avoid noise for no signal samples by computeFilteredVectors.
save	: Save files after each step

Details

buildMgsFinal

Value

a list containing the final elements such as the 50 most connected genes, the mean vectors etc

Author(s)

Edi Prifti

eprifti/momr documentation built on Sept. 27, 2022, 3:36 a.m.