fisher.iteration will test a candidate gene list for
overrepresenation in the various cell type/pSI threshold
combinations produced by the specificty.index function.
NOTE:Supplementary data (human & mouse expression sets,
calculated pSI datasets, etc.) can be found in
pSI.data package located at the following URL:
data frame output from
candidate gene list tested for overrepresentation in cell types/samples. Comprised of official gene symbols.
character string used to indicate what
background gene list should be used in Fisher's exact
test for overrepresentation. The default value is
logical. default output is bonferroni
corrected p-value but if
This function is used to answer the question of what is the probability that a certain number of genes specific to a certain cell type/sample occured by chance (as usual with low probabilities corresponding to high statistical significance). This is accomplished with a binary variable for each gene in the population with two mutual exclusive values: 1) The gene is specific to the cell type/sample in question or 2) The gene is not specific to the cell type/sample in question
Xiaoxiao Xu, Alan B. Wells, David OBrien, Arye Nehorai, Joseph D. Dougherty
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##load sample pSI output data(sample.data) ##load sample candidate gene lists data(candidate.genes) ##run Fisher's exact test for overrperesentation on pSI.out for the AutDB ##candidate gene list across all cell types/sample types & pSI thresholds fisher.out.AutDB <- fisher.iteration(pSIs=sample.data$pSI.output, candidate.genes=candidate.genes$AutDB)
Loading required package: gdata sh: 1: cannot create /dev/null: Permission denied gdata: Unable to locate valid perl interpreter gdata: gdata: read.xls() will be unable to read Excel XLS and XLSX files gdata: unless the 'perl=' argument is used to specify the location of a gdata: valid perl intrpreter. gdata: gdata: (To avoid display of this message in the future, please ensure gdata: perl is installed and available on the executable search path.) sh: 1: cannot create /dev/null: Permission denied gdata: Unable to load perl libaries needed by read.xls() gdata: to support 'XLX' (Excel 97-2004) files. gdata: Unable to load perl libaries needed by read.xls() gdata: to support 'XLSX' (Excel 2007+) files. gdata: Run the function 'installXLSXsupport()' gdata: to automatically download and install the perl gdata: libaries needed to support Excel XLS and XLSX formats. Attaching package: 'gdata' The following object is masked from 'package:stats': nobs The following object is masked from 'package:utils': object.size The following object is masked from 'package:base': startsWith
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