Man pages for databio/PCRSA
Coordinate Covariation Analysis

aggregateLoadingsUse PCA loadings to score a region set
atf3_chr1Atf3 binding regions.
brcaLoadings1A matrix with loadings
brcaMCoord1A data.frame object with coordinates for cytosines from chr1...
brcaMethylData1A matrix with DNA methylation levels from chromosome 1 for...
brcaPCScoresA matrix with principal component scores for PCs 1-4 for four...
brcaPCScores657A data.frame with principal component scores for PCs 1-4 for...
COCOACoordinate Covariation Analysis (COCOA)
esr1_chr1Estrogen receptor alpha binding regions.
gata3_chr1Gata3 binding regions.
getLoadingProfileCreate a "meta-region" loading profile
nrf1_chr1Nrf1 binding regions.
regionQuantileByPCVisualize how individual regions are associated with...
rsRankingIndexGet indices for top scored region sets
rsScoreHeatmapHeatmap of region set scores
rsScoresExample COCOA Results (made up)
runCOCOADo COCOA with many region sets
signalAlongPCVisualize how genomic signal in a region set changes along...
databio/PCRSA documentation built on Dec. 7, 2018, 8:57 a.m.