Man pages for hfang-bristol/Pi
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

cTargetDefinition for S3 class 'cTarget'
dTargetDefinition for S3 class 'dTarget'
eGSEADefinition for S3 class 'eGSEA'
eTargetDefinition for S3 class 'eTarget'
pNodeDefinition for S3 class 'pNode'
pPerfDefinition for S3 class 'pPerf'
sGSDefinition for S3 class 'sGS'
sTargetDefinition for S3 class 'sTarget'
xContourFunction to visualise a numeric matrix as a contour plot
xGSEAbarplotFunction to visualise GSEA results using a barplot
xGSEAconciserFunction to make GSEA results conciser by removing redundant...
xGSEAdotplotFunction to visualise GSEA results using dot plot
xGSsimulatorFunction to simulate gold standard negatives (GSN) given gold...
xMLcaretFunction to integrate predictor matrix in a supervised manner...
xMLcompareFunction to visualise cross-validation performance against...
xMLdensityFunction to visualise machine learning results using density...
xMLdotplotFunction to visualise machine learning results using dot plot
xMLfeatureplotFunction to visualise/assess features used for machine...
xMLglmnetFunction to integrate predictor matrix in a supervised manner...
xMLparametersFunction to visualise cross-validation performance against...
xMLrandomforestFunction to integrate predictor matrix in a supervised manner...
xMLrenameFunction to rename predictors used in machine learning
xMLzoomFunction to visualise machine learning results using zoom...
xPCHiCplotFunction to visualise promoter capture HiC data using...
xPieplotFunction to visualise data frame using pie plots
xPierFunction to do prioritisation through random walk techniques
xPierAnnoFunction to prioritise seed genes only from a list of pNode...
xPierCorFunction to calculate correlation between prioritised genes...
xPierCrossFunction to extract priority matrix from a list of...
xPierEvidenceFunction to extract evidence from a list of pNode objects
xPierGenesFunction to prioritise genes from an input network and the...
xPierGRsFunction to prioritise genes given a list of genomic regions
xPierGSEAFunction to prioritise pathways based on GSEA analysis of...
xPierKEGGFunction to visualise prioritised genes in terms of a KEGG...
xPierManhattanFunction to visualise prioritised genes using manhattan plot
xPierMatrixFunction to extract priority or evidence matrix from a list...
xPierPathwaysFunction to prioritise pathways based on enrichment analysis...
xPierROCRFunction to assess the dTarget performance via ROC and...
xPierSNPsFunction to prioritise genes given a list of seed SNPs...
xPierSNPsAdvFunction to prepare genetic predictors given a list of seed...
xPierSNPsConsensusFunction to resolve relative importance of distance weight...
xPierSubnetFunction to identify a gene network from top prioritised...
xPierTrackFunction to visualise a prioritised gene using track plot
xPierTrackAdvFunction to visualise a list of prioritised genes using...
xPredictCompareFunction to compare prediction performance results
xPredictROCRFunction to assess the prediction performance via ROC and...
xRWRFunction to implement Random Walk with Restart (RWR) on the...
xSNP2cGenesFunction to define HiC genes given a list of SNPs
xSNP2eGenesFunction to define eQTL genes given a list of SNPs or a...
xVisEvidenceFunction to visualise evidence for prioritised genes in a...
xVisEvidenceAdvFunction to visualise evidence and priority scores for...
hfang-bristol/Pi documentation built on May 28, 2018, noon