Man pages for rmflight/ccPaper
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| calcFraction | calculate fraction of genes annotated to GO terms |
| collapseProbes | collapse probes to genes |
| cucCCOutput.RData | cucCCOutput.RData |
| cucCCOutPut.RData | cucCCOutPut.RData |
| cucRomer.RData | cucRomer.RData |
| diffGOStats | calculate difference between noise and clean differences for... |
| fishersMethod | fishers method for combining p-values |
| getDiffGenes | get differentially expressed genes in a data.frame |
| goSample | generate GO sample with genes |
| gseaDiffs | results and diffs following genesettest |
| gseaProportion | generates proportion of genes in top 50 |
| gseaProportionFisher | gseaProportion, combined using Fisher's method |
| gseaProportionMax | gseaProportion combining using max p-value |
| gseaProportionVary | vary gsea proportion |
| gseaSizeRange | generate entries within a distribution |
| hyperGOMultiEnrichment | hyperGOMultiEnrichment |
| limitedRandomSample | returns random sample between limits |
| lung.RData | lung.RData |
| mmGeneSetTest | multiple-multiple geneSetTests |
| multicontrastRomer | multicontrast romer |
| multiGeneSetTest | run multiple geneSetTest's |
| multiSampleGeneSetTest | run geneSetTest for multiple samples |
| muscle_data.RData | muscle_data.RData |
| muscleGeneSetTest.RData | muscleGeneSetTest.RData |
| muscleRomer.RData | muscleRomer.RData |
| noiseSamples.RData | noiseSamples.RData |
| noiseSweepRes.RData | noiseSweepRes.RData |
| p2signed | apply regression model to pvalues |
| possibleNoise | possible noise genes to sample from |
| pvalueDiffSig | calculate difference and significance |
| pvaluesMultiEnrich | get p-values from multiple enrichments |
| rankGenes | rank genes using limma |
| sameGOStats | calculate statistics for all the same GO terms across... |
| samplePValueGenGSEA | change set of p-values for GSEA |
| sampleTerms | samples genes from GO |
| sampletValueGenGSEA | change set of t-values for GSEA |
| skinGeneSetTest.RData | skinGeneSetTest.RData |
| skinMuscleCCOutput.RData | skinMuscleCCOutput.RData |
| skin_rma_data.RData | skin_rma_data.RData |
| skinRomer.RData | skinRomer.RData |
| sweepNoiseSample | Different values of noise |
| trimGOFrac | trim go2gene and get fractions |
| uc_crohns_rawData.RData | uc_crohns_rawData.RData |
