Candidate Gene Overlap

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Description

candidate.overlap Extracts genes specific to samples which overlap with a candidate gene list at various pSI thresholds

Usage

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Arguments

pSIs

data frame output from specificity.index function with the number of columns equal to the number of samples and genes as rows.

candidate.genes

candidate gene list tested for overrepresentation in cell types/samples. Comprised of official gene symbols.

write.csv

logical variable indicating if csv files will be written to the current working directory (default value is FALSE)

Details

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: http://genetics.wustl.edu/jdlab/psi_package/

Author(s)

Xiaoxiao Xu, Alan B. Wells, David OBrien, Arye Nehorai, Joseph D. Dougherty

Examples

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##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)