sysbio-curie / acsnminer Goto Github PK

library(devtools)
Message d'avis :
le package ‘devtools’ a été compilé avec la version R 3.1.3
install_github('sysbio-curie/ACSN_Enrichment')
Downloading github repo sysbio-curie/ACSN_Enrichment@master
Installing ACSN_Enrichment
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore CMD INSTALL
'/private/var/folders/7l/0rp_x4dd74n4hv3hl1m6rrbw0000gr/T/RtmpCGyZAS/devtools103414d08f71/sysbio-curie-ACSN_Enrichment-b9e9909'
--library='/Library/Frameworks/R.framework/Versions/3.1/Resources/library'
--install-tests

• installing source package ‘ACSN_Enrichment’ ...
  Error : Fichier DESCRIPTION incorrect

Nom de package mal orthographié

Voyez l'information à propos des fichiers DESCRIPTION dans la section
'Creating R packages' du manuel 'Writing R Extensions'.

ERROR: installing package DESCRIPTION failed for package ‘ACSN_Enrichment’

• removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/ACSN_Enrichment’
  Erreur : Command failed (1)

add the following features to results table:

• Universe size
• Nb genes in universe

Just so we agree on the definitions... Should we:

• If universe = ACSN: should we downsize the gene list to the ones that are in ACSN?
• Same question if universe is user input

Possible correction for multiple testing:

• Bonferroni
• Benjamini Hochberg
• FDR

Which should we implement? All?

module
module_size
nb_genes_in_module
genes_in_module
universe_size
nb_genes_in_universe
p.value
p.value.corrected

Think it's good practise, so it should be enabled by default, although the user shuld be able to disable it.

Put the list in a 'global' list once in the code, so that when we add new maps, we do not have to change the code in multiple places.

The issue is the following:
http://stackoverflow.com/questions/18922493/how-can-you-read-a-csv-file-in-r-with-different-number-of-columns

As stated, read.csv only uses the first 5 lines to determine the number of columns... Hence the issue. I'll dig into that and correct the import code.

As the title says!
;-)