This package contains functions to read GSE raw data and returns a tidy format. It’s especially useful for chip annotation file, the format of which is really in a messy. You just need to provide the raw data file and it will give you a nice table containing probes and HUGO gene symbols.
if (!('devtools' %in% .packages(T))) install.packages('devtools');
remotes::install_github('dongzhuoer/thesis/r-lib/rGEO');Inpatient people please refer to vignette('rGEO').
For why this package, read this
vignette('probe2symbol').
Wired as it seems, it’s best way I can think about so far to maintain reproducibility.
Basically, you make change in R/platform.R,
Load All (C-S-L, or ), then Knit
R-raw/platform.Rmd to check whether the rule returns
exactly what you want. (you can also execute all chunk before, and then
repeat modify rule - load- run a specific chunk to save time)