xContour |
Function to visualise a numeric matrix as a contour plot |
xGSsimulator |
Function to simulate gold standard negatives (GSN) given gold standard positives (GSP) and a gene network |
xMLdensity |
Function to visualise machine learning results using density plot |
xMLdotplot |
Function to visualise machine learning results using dot plot |
xMLrandomforest |
Function to integrate predictor matrix in a supervised manner via machine learning algorithm random forest. |
xPCHiCplot |
Function to visualise promoter capture HiC data using different network layouts |
xPier |
Function to do prioritisation through random walk techniques |
xPierGenes |
Function to prioritise genes from an input network and the weight info imposed on its nodes |
xPierManhattan |
Function to visualise prioritised genes using manhattan plot |
xPierMatrix |
Function to extract priority matrix from a list of pNode objects |
xPierPathways |
Function to prioritise pathways based on enrichment analysis of top prioritised genes |
xPierSNPs |
Function to prioritise genes given a list of seed SNPs together with the significance level (e.g. GWAS reported p-values) |
xPierSNPsAdv |
Function to prepare genetic predictors given a list of seed SNPs together with the significance level (e.g. GWAS reported p-values) |
xPierSNPsConsensus |
Function to resolve relative importance of distance weight and eQTL weight priorising consensus gene ranks given a list of seed SNPs together with the significance level (e.g. GWAS reported p-values) |
xPierSubnet |
Function to identify a gene network from top prioritised genes |
xPierTrack |
Function to visualise prioritised genes using track plot |
xPredictCompare |
Function to compare prediction performance results |
xPredictROCR |
Function to assess the prediction performance via ROC and Precision-Recall (PR) analysis |
xRWR |
Function to implement Random Walk with Restart (RWR) on the input graph |
xSNP2cGenes |
Function to define HiC genes given a list of SNPs |
xSNP2eGenes |
Function to define eQTL genes given a list of SNPs or a customised eQTL mapping data |
xSNPeqtl |
Function to extract eQTL-gene pairs given a list of SNPs or a customised eQTL mapping data |
xSNPhic |
Function to extract promoter capture HiC-gene pairs given a list of SNPs |