Man pages for arcolombo/junk
qusage: Quantitative Set Analysis for Gene Expression
| absoluteTest | absolute test homogeneity score |
| absoluteTest.genePvals | A function to calculate the P values for each gene as... |
| absoluteTest.genePvalsFAST | function to calculate the homogeneity P value faster |
| aggregateGeneSet | Calculate Pathway Activation |
| aggregateGeneSetArm | Combine individual gene differential expresseion for each... |
| approximatedNu | Nu values approximated, this is a vector holding constants |
| calcBayesCI | Calculate pathway Confidence Intervals |
| calcPCor | A function to calculate the Variance Inflation Factor (VIF)... |
| calcVIF | Calculate Variance Inflation Factor |
| combinePDFs | Combine PDFs from multiple QuSAGE comparisons |
| compareTwoDistsFaster | Compute p-value of two distributions not centered at zero |
| eset.full | Example gene expression set |
| filterGenes | Filter out genes with SD lower than a threshold and mean... |
| fluVaccine | Gene expression sets from Flu Vaccine trials |
| GeneSets | Example Gene Sets |
| getExAbs | approximates Nu values |
| getXcoords | Get the X coordinates for the points of the PDF |
| homogeneityScore | homogenity score |
| makeComparison | Compare Genes Between Two Groups |
| multi_conv | fast fourier transform method |
| newQSarray | The qusage Array Object |
| Ni | helper funciton to calculate DOF |
| pdfScaleFactor | calculate a scaling factor to multiply the PDF by (so that it... |
| plotCIs | Plot Pathway Mean and Confidence Intervals |
| plotCIsGenes | Plot Gene Mean and Confidence Intervals |
| plotCombinedPDF | Plot combined PDF for an individual pathway |
| plotDensityCurves | Plot gene set PDFs |
| plotGeneSetDistributions | Plot gene and gene set PDFs |
| pVal | Calculate p-values for gene set activity |
| qgen | Run qusage while incoprating generalized least squares and... |
| QSarray-class | Class '"QSarray"' |
| qsTable | Summary of QSarray Results |
| qusage | Run qusage on an expression dataset |
| qusageArm | This file contains the primary code for the qusage... |
| qusageCutArm | This file contains the primary code for the qusage... |
| quslmFit | LINEAR MODELS used for qusage calls the stats lm.fit call and... |
| read.gmt | Read in gene set information from .gmt files |
