Description Usage Arguments Value Progress updates Parallel processing Examples
View source: R/compile_by_organism.R
Compile Ramani HiC Data Files into Data Frames stored in RDS files
1 2 3 4 5 6 | compile_by_organism(
samples,
organisms = c("human", "mouse"),
path = file.path("hicData", "GSE84920"),
path_dest = "compiledData"
)
|
samples |
A character vector of K sample names. |
organisms |
A character vector of N organism names. |
path |
The folder where the input HiC data files ‘*.percentages,validPairs.txt.gz’ are located. |
path_dest |
The folder where the compiled RDS files should be saved. |
An K-by-N character matrix of pathnames of RDS files. Each RDS file contains a data.frame.
This function signals progressr::progression updates. To visualize, or in other ways render, progress information, wrap the call inside a progressr::with_progress call.
This function supports processing of (organism, sample):s in parallel
via the future framework.
For example, setting future::plan("multisession")
will parallelize
on the local machine.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## Not run:
progressr::with_progress({
files <- TopDomStudy::compile_by_organism(
samples=c("GSM2254215_ML1", "GSM2254219_PL2",
"GSM2254216_ML2", "GSM2254218_PL1"),
organisms="human",
path="hicData/GSE84920", path_dest="compiledData"
)
})
print(files)
# human
# GSM2254215_ML1 "compiledData/GSM2254215_ML1,human,unique.rds"
# GSM2254219_PL2 "compiledData/GSM2254219_PL2,human,unique.rds"
# GSM2254216_ML2 "compiledData/GSM2254216_ML2,human,unique.rds"
# GSM2254218_PL1 "compiledData/GSM2254218_PL1,human,unique.rds"
## End(Not run)
|
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