“I would like to change the default maps that are computed in ACSNMineR” or “ACSN maps have a new version, and I would like to update it before the package release.”
ACSN maps are stored as a list of dataframes generated by:
format_from_gmt They were exported using the R function “save” in the package folder “data/ACSN_maps.rda”. Changing this package and re-installing the modified ACSNMineR will thus change the maps on which enrichment is computed.
BEWARE Once your map will be updated, the names that can be used as map argument in the enrichment function will be changed too! In R the name of your map list should be ACSN_maps
If your working directory in the package main directory:
save(list = "ACSN_maps",file = "data/ACSN_maps.rda")Note that the name of the variable should be provided to save not the variable itself.
If you don’t know where your working directory is, you can get the information with getwd() and change it with
setwd("path/to/package")Now you only have to load devtools and install the package:
library("devtools")
install("/path/to/modified/ACSNMineR") library("ACSNMineR")