Description Usage Arguments Details Author(s) Examples
View source: R/candidate.overlap.R
candidate.overlap Extracts genes specific to samples
which overlap with a candidate gene list at various pSI
candidate.overlap(pSIs, candidate.genes, write.csv = FALSE)
data frame output from
candidate gene list tested for overrepresentation in cell types/samples. Comprised of official gene symbols.
logical variable indicating if csv files will be written to the current working directory (default value is FALSE)
Returns list consisting of 6 data frames, one for each pSI
threshold. Each data frame contains genes specific to each
sample which overlap with a candidate gene list and whose
pSI values fall below each respective threshold for each
cell type/sample included in the analysis.
NOTE:Supplementary data (human & mouse expression sets,
calculated pSI datasets, etc.) can be found in
pSI.data package located at the following URL:
Xiaoxiao Xu, Alan B. Wells, David OBrien, Arye Nehorai, Joseph D. Dougherty
1 2 3 4 5 6 7
##load sample pSI output data(sample.data) ##load sample candidate gene lists data(candidate.genes) ##Generates lists of overlapping genes candidate.gene.overlap.AutDB <- candidate.overlap(pSIs=sample.data$pSI.output, candidate.genes=candidate.genes$AutDB)
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