Candidate Gene Overlap

candidate.overlap extracts the genes specific to each cell type/sample (as listed by pSI.list) that are also present in a candidate gene list, at each of the four standard pSI thresholds (0.05, 0.01, 0.001 and 0.0001).

Usage

candidate.overlap(pSIs, candidate.genes, write.csv = FALSE)

Arguments

pSIs

data frame output from specificity.index, with one column per cell type/sample and genes as rows.

candidate.genes

character vector of official gene symbols to test for overlap with the cell type-specific genes.

write.csv

logical. If TRUE, one CSV file per threshold (pSi_0.0001.csv, pSi_0.001.csv, pSi_0.01.csv, pSi_0.05.csv) is written to the current working directory. Default FALSE.

Value

A named list of four data frames (pSi_0.0001, pSi_0.001, pSi_0.01, pSi_0.05), one per pSI threshold, with one column per cell type/sample listing the candidate genes that are specific to it at that threshold, padded with NA.

Details

Gene symbols are compared in upper case, so mouse and human symbols can be matched against each other. (Before pSI 1.2.0 only the pSIs row names were upper-cased, so lower-case candidate symbols silently never matched.)

See also

fisher.iteration to test whether each overlap is larger than expected by chance.

Author

Xiaoxiao Xu, Alan B. Wells, David R. O'Brien, Arye Nehorai, Joseph D. Dougherty

Examples

##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)
candidate.gene.overlap.AutDB$pSi_0.01
#>   Amygdala.Young.Adulthood_0.01 Cerebellum.Young.Adulthood_0.01
#> 1                            NA                          CADPS2
#> 2                            NA                             EN2
#> 3                            NA                            RELN
#>   Cortex.Young.Adulthood_0.01 Hippocampus.Young.Adulthood_0.01
#> 1                       MEF2C                            FEZF2
#> 2                        <NA>                             <NA>
#> 3                        <NA>                             <NA>
#>   Striatum.Young.Adulthood_0.01 Thalamus.Young.Adulthood_0.01
#> 1                       ADORA2A                         NTNG1
#> 2                          <NA>                          <NA>
#> 3                          <NA>                          <NA>