runCOCOA: Run COCOA: quantify inter-sample variation, score region sets

In databio/PCRSA: Coordinate Covariation Analysis

Run COCOA: quantify inter-sample variation, score region sets

Description

This is a convenience function that does the two steps of COCOA: quantifying the epigenetic variation and scoring the region sets. This function will return the real COCOA scores if using the default 'sampleOrder' parameter values. This function also makes it easy to generate null distributions in order to evaluate the statistical significance of the real COCOA results. You can use the sampleOrder parameter to shuffle the samples, then run COCOA to get fake scores for each region set. By doing this many times, you can build a null distribution for each region set composed of the region set's random scores from each permutation. There are multiple options for quantifying the epigenetic variation, specified by the 'variationMetric' parameter. Quantifying the variation for the real/non-permuted COCOA scores should be done with the same variation metric as is used for the random permutations. For an unsupervised analysis using dimensionality reduction, first, the dimensionality reduction is done outside 'runCOCOA', then the latent factors/principal components are input to 'runCOCOA' as the sample labels (targetVar parameter) when calculating both the real and also the permutated region set scores. For a supervised analysis, the target variables/phenotypes are the targetVar. See the vignettes for examples.

Usage

runCOCOA(
  genomicSignal,
  signalCoord,
  GRList,
  signalCol,
  targetVar,
  sampleOrder = 1:nrow(targetVar),
  variationMetric = "cor",
  scoringMetric = "default",
  verbose = TRUE,
  absVal = TRUE,
  olList = NULL,
  pOlapList = NULL,
  centerGenomicSignal = TRUE,
  centerTargetVar = TRUE,
  returnCovInfo = TRUE
)

Arguments

genomicSignal	Matrix/data.frame. The genomic signal (e.g. DNA methylation levels) Columns of genomicSignal should be samples/patients. Rows should be individual signal/features (each row corresponds to one genomic coordinate/range)
signalCoord	A GRanges object or data frame with coordinates for the genomic signal/original epigenetic data. Coordinates should be in the same order as the original data and the feature contribution scores (each item/row in signalCoord corresponds to a row in signal). If a data.frame, must have chr and start columns (optionally can have end column, depending on the epigenetic data type).
GRList	GRangesList object. Each list item is a distinct region set to test (region set: regions that correspond to the same biological annotation). The region set database must be from the same reference genome as the coordinates for the actual data/samples (signalCoord).
signalCol	A character vector with the names of the sample variables of interest/target variables (e.g. PCs or sample phenotypes). The columns in 'sampleLabels' for which to calculate the variation related to the epigenetic data (e.g. correlation) and then to run COCOA on.
targetVar	Matrix or data.frame. Rows should be samples. Columns should be the target variables (whatever variable you want to test for association with the epigenetic signal: e.g. PC scores),
sampleOrder	numeric. A vector of length (number of samples). If sampleOrder is 1:(number of samples) then this function will return the real COCOA scores. To generate random COCOA scores in order to make null distributions, shuffle the samples in a random order. E.g. sampleOrder = sample(1:ncol(genomicSignal), ncol(genomicSignal)) where ncol(genomicSignal) is the number of samples. Set the seed with set.seed() before making sampleOrder to ensure reproducibility.
variationMetric	Character. The metric to use to quantify the association between each feature in genomicSignal and each target variable in sampleLabels. Either "cor" (Pearson correlation), "cov" (covariation), or "spearmanCor" (Spearman correlation).
scoringMetric	A character object with the scoring metric. There are different methods available for signalCoordType="singleBase" vs signalCoordType="multiBase". For "singleBase", the available methods are "regionMean", "regionMedian", "simpleMean", and "simpleMedian". The default method is "regionMean". For "multiBase", the methods are "proportionWeightedMean", "simpleMean", and "simpleMedian". The default is "proportionWeightedMean". "regionMean" is a weighted average of the signal, weighted by region (absolute value of signal if absVal=TRUE). First the signal is averaged within each regionSet region, then all the regions are averaged. With "regionMean" method, be cautious in interpretation for region sets with low number of regions that overlap signalCoord. The "regionMedian" method is the same as "regionMean" but the median is taken at each step instead of the mean. The "simpleMean" method is just the unweighted average of all (absolute) signal values that overlap the given region set. For multiBase data, this includes signal regions that overlap a regionSet region at all (1 base overlap or more) and the signal for each overlapping region is given the same weight for the average regardless of how much it overlaps. The "simpleMedian" method is the same as "simpleMean" but takes the median instead of the mean. "proportionWeightedMean" is a weighted average of all signalCoord regions that overlap with regionSet regions. For each signalCoord region that overlaps with a regionSet region, we calculate what proportion of the regionSet region is covered. Then this proportion is used to weight the signal value when calculating the mean. The denominator of the mean is the sum of all the proportion overlaps.
verbose	A "logical" object. Whether progress of the function should be shown. One bar indicates the region set is completed.
absVal	Logical. If TRUE, take the absolute value of values in signal. Choose TRUE if you think there may be some genomic loci in a region set that will increase and others will decrease (if there may be anticorrelation between regions in a region set). Choose FALSE if you expect regions in a given region set to all change in the same direction (all be positively correlated with each other).
olList	list. Each list item should be a "SortedByQueryHits" object (output of findOverlaps function). Each hits object should have the overlap information between signalCoord and one item of GRList (one unique region set). The region sets from GRList must be the "subject" in findOverlaps and signalCoord must be the "query". E.g. findOverlaps(subject=regionSet, query=signalCoord). Providing this information can greatly improve permutation speed since the overlaps will not have to be calculated for each permutation. The "runCOCOAPerm" function calculates this information only once, internally, so this does not have to be provided when using that function. When using this parameter, signalCoord, genomicSignal, and each region set must be in the same order as they were when olList was created. Otherwise, the wrong genomic loci will be referenced (e.g. if epigenetic features were filtered out of genomicSignal after olList was created.)
pOlapList	list. This parameter is only used if the scoring metric is "proportionWeightedMean" and olList is also provided as an argument. Each item of the list should be a vector that contains the proportion overlap between signalCoord and regions from one region set (one item of GRList). Specifically, each value should be the proportion of the region set region that is overlapped by a signalCoord region. The proportion overlap values should be in the same order as the overlaps given by olList for the corresponding region set.
centerGenomicSignal	Logical. Should rows in genomicSignal be centered based on their means? (subtracting row mean from each row)
centerTargetVar	Logical. Should columns in targetVar be centered based on their means? (subtract column mean from each column)
returnCovInfo	logical. If TRUE, the following coverage and region set info will be calculated and included in function output: regionSetCoverage, signalCoverage, totalRegionNumber, and meanRegionSize. For the proportionWeightedMean scoring method, sumProportionOverlap will also be calculated.

Value

data.frame. The output of aggregateSignalGRList for one permutation.

Examples

data("esr1_chr1")
data("nrf1_chr1")
data("brcaMethylData1")
data("brcaMCoord1")
pcScores <- prcomp(t(brcaMethylData1))$x
targetVarCols <- c("PC1", "PC2")
targetVar <- pcScores[, targetVarCols]

# give the actual order of samples to `runCOCOA` to get the real scores
correctSampleOrder=1:nrow(targetVar)
realRSScores <- runCOCOA(genomicSignal=brcaMethylData1,
                        signalCoord=brcaMCoord1,
                        GRList=GRangesList(esr1_chr1, nrf1_chr1),
                        signalCol=c("PC1", "PC2"),
                        targetVar=targetVar,
                        sampleOrder=correctSampleOrder,
                        variationMetric="cor")
realRSScores
        
# give random order of samples to get random COCOA scores 
# so you start building a null distribution for each region set 
# (see vignette for example of building a null distribution with `runCOCOA`)
randomOrder <- sample(1:nrow(targetVar), 
                      size=nrow(targetVar),
                      replace=FALSE)
randomRSScores <- runCOCOA(genomicSignal=brcaMethylData1,
                          signalCoord=brcaMCoord1,
                          GRList=GRangesList(esr1_chr1, nrf1_chr1),
                          signalCol=c("PC1", "PC2"),
                          targetVar=targetVar,
                          sampleOrder=randomOrder,
                          variationMetric="cor")
randomRSScores

databio/PCRSA documentation built on Sept. 2, 2023, 11:24 p.m.