Convert pSI output to gene counts

pSI.count counts the number of genes specific to each cell type/sample at each of the four standard pSI thresholds (0.05, 0.01, 0.001 and 0.0001).

Usage

pSI.count(pSIs, write.csv = FALSE)

Arguments

pSIs

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

write.csv

logical. If TRUE, the table is also written to gene_count_1.csv in the current working directory. Default FALSE.

Value

A data frame with four rows, one per pSI threshold ("0.0001", "0.001", "0.01", "0.05"), and one column per cell type/sample, giving the number of genes whose pSI value falls below each threshold.

See also

pSI.list for the gene lists themselves.

Author

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

Examples

##load sample pSI output
data(sample.data)
##Count the number of genes specific to each cell type/sample type across all pSI thresholds
pSI.out.count <- pSI.count(pSIs=sample.data$pSI.output)
pSI.out.count
#>        Amygdala.Young.Adulthood Cerebellum.Young.Adulthood
#> 0.0001                        0                         19
#> 0.001                         0                         32
#> 0.01                          0                         84
#> 0.05                         10                        230
#>        Cortex.Young.Adulthood Hippocampus.Young.Adulthood
#> 0.0001                      1                           1
#> 0.001                       3                           5
#> 0.01                       20                          15
#> 0.05                       90                          29
#>        Striatum.Young.Adulthood Thalamus.Young.Adulthood
#> 0.0001                        2                        5
#> 0.001                         8                        9
#> 0.01                         29                       32
#> 0.05                        116                       85