|
aggregateSignal()
|
Score a region set using feature contribution scores |
|
aggregateSignalGRList()
|
Score many region sets |
|
atf3_chr1
|
Atf3 binding regions. |
|
brcaATACCoord1
|
A GRanges object with coordinates for select
BRCA ATAC-seq peak regions from chr1. |
|
brcaATACData1
|
A matrix with ATAC-seq counts in select peak regions
from chromosome 1 for 37 patients. |
|
brcaMCoord1
|
A GRanges object with genomic coordinates for cytosines
from chr1 for the package's built-in DNA methylation data |
|
brcaMetadata
|
A data.frame with patient metadata for breast
cancer patients. |
|
brcaMethylData1
|
A matrix with DNA methylation levels
from some CpGs on chromosome 1 |
|
brcaPCScores
|
A matrix with principal component scores for
PCs 1-4 for four breast cancer patients. |
|
brcaPCScores657
|
A data.frame with principal component scores for
PCs 1-4 for 657 breast cancer patients as well
as a column with estrogen receptor status. |
|
COCOA
|
Coordinate Covariation Analysis (COCOA) |
|
convertToFromNullDist()
|
Converts COCOA permutation results to null distributions and vice versa |
|
esr1_chr1
|
Estrogen receptor alpha binding regions. |
|
gata3_chr1
|
Gata3 binding regions. |
|
getGammaPVal()
|
Get a p-value for region set scores based on a gamma distribution. |
|
getMetaRegionProfile()
|
Create a "meta-region" profile |
|
getPermStat()
|
Get p-value or z-score based on permutation results |
|
getTopRegions()
|
Get regions that are most associated with target variable |
|
nrf1_chr1
|
Nrf1 binding regions. |
|
plotAnnoScoreDist()
|
Plot ranked region set scores, annotating groups of interest |
|
regionQuantileByTargetVar()
|
Visualize how individual regions are associated with target variable |
|
rsRankingIndex()
|
Get indices for top scored region sets |
|
rsScoreHeatmap()
|
Heatmap of region set scores |
|
rsScores
|
Example COCOA Results (made up) |
|
runCOCOA()
|
Run COCOA: quantify inter-sample variation, score region sets |
|
runCOCOAPerm()
|
Run COCOA permutations to get p-values |
|
signalAlongAxis()
|
Visualize how genomic signal in a region set changes
along a given axis |