View source: R/easyDifferentialGeneCoexpression.r
easyDifferentialGeneCoexpression | R Documentation |
Function that computes the differential coexpression of a list of probesets in a specific dataset and returns the most significant pairs
easyDifferentialGeneCoexpression( list_of_probesets_to_select, GSE_code, featureNameToDiscriminateConditions, firstConditionName, secondConditionName, batchCorrection = TRUE, verbose = FALSE )
list_of_probesets_to_select |
list of probesets for which the differential coexpression should be computed |
GSE_code |
GEO accession code of the dataset to analyze |
featureNameToDiscriminateConditions |
name of the feature of the dataset that contains the two conditions to investigate |
firstConditionName |
name of the first condition in the feature to discriminate (for example, "healthy") |
secondConditionName |
name of the second condition in the feature to discriminate (for example, "cancer") |
batchCorrection |
says if the script should perform the batch correction with limma::removeBatchEffect() or not |
verbose |
prints all the intermediate message to standard output or not |
a dataframe containing the significantly differentially co-expressed pairs of genes
probesetList <- c("200738_s_at", "217356_s_at", "206686_at") verboseFlag <- "TRUE" batchCorrection <- "TRUE" signDiffCoexpressGenePairs <- easyDifferentialGeneCoexpression(probesetList, "GSE3268", "description", "Normal", "Tumor", verboseFlag)
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