Description Usage Arguments Details Value Author(s) References See Also Examples
This function is intended to compare a new genomics dataset to existing primary genomics data by using the Generalized Random Set approach to compute the concordance of gene lists based on corresponding p-values.
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reference.p |
Reference p-values. A vector, a matrix with two columns where the first column contains the geneIDs and the second column contains the p-values, or a matrix with three columns where the first column contains the geneIDs, the second contains the scores and the third contains probability. If the reference.p is a vector and reference.gL is NULL, query.p and reference.p are assumed to have the same number of genes and genes are in the same order. |
query.gL |
If query.p is a vector of p-values, this parameters is expected to contain a vector of corresponding gene IDs of same length. Otherwise it is ignored. |
reference.gL |
If reference.p is a vector of p-values, this parameters is expected to contain a vector of corresponding gene IDs of same length. Otherwise it is ignored. |
na.rm |
If TRUE, any NA's in query.p and/or reference.p are removed before computing the GRS score. |
estimateNullDistr |
If TRUE, an empirical distribution of the gene-specific GRS score is estimated. |
nullDistrQuantiles |
If 'estimateNullDistr' is TRUE, specifies the desired quantiles of the null-distribution. |
nullDistrN |
If 'estimateNullDistr' is TRUE, specifies the number of iterations for the estimation function. |
tolerateWarnings |
If FALSE, function returns (with the warning message as character string). This parameter is intended when using GRS() by the Genomics Portals. |
pAdjust.method.query |
If NULL, the probability of differential expression is set to posterior probability of diff expression based on query.p, else 1-adjusted pvalue is used from the p.adjust function. |
pAdjust.method.reference |
If NULL, the probability of differential expression is set to posterior probability of diff expression based on reference.p, else 1-adjusted pvalue is used from the p.adjust function. |
lambda |
To be passed to qvalue() function which estimates the proportion of non-differentially expressed genes. |
rescale |
If TRUE (default) quantile normalization is performed between scores and probabilities of differential gene expression and TREG binding profiles. |
cquery.p |
Query p-values. A vector, a matrix with two columns where the first column contains the geneIDs and the second column contains the p-values, or a matrix with three columns where the first column contains the geneIDs, the second contains the scores and the third contains probability. If the query.p is a vector and query.gL is NULL, query.p and reference.p are assumed to have the same number of genes and genes are in the same order. |
This function is intended to compare a new genomics dataset to existing primary genomics data by using the Generalized Random Set approach to compute the concordance of gene lists based on corresponding p-values.
This function returns a list: p.value : GRS p-value. Under the null-hypothesis, the two gene lists are not concordant.
z.score : GRS z-score
geneTable: Table where the first column contains the common gene IDs and the second column contains the geney-specific GRS score.
EvalueNullDistrQ: If 'estimateNullDistr' is TRUE, this list item gives the quantiles of the null-distribution specified by 'nullDistrQuantiles' parameter.
Johannes Freudenberg, Mehdi Fazel-Najafabadi
...
<e2><80><98>convertGeneTable<e2><80><99>, <e2><80><98>runCLEAN<e2><80><99>, <e2><80><98>LRpath<e2><80><99>
1 2 3 4 5 6 7 8 9 | ## Not run
data(erAlpha)
data(erExpression)
refTable <- GenomicFeatures::makeTxDbFromUCSC(genome="hg19",tablename="refGene")
ChipSeq <- annotateChipSeqPeaks(chip.seq=erAlpha[[3]],transcriptDB=refTable,distanceRange=c(-1e+06,1e+06))
tregBindingERalpha <- chipSeqWeightedSum(ChipSeq,verbose=TRUE, genome=refTable)
bindingExpressionConcordance <- tregGRS(query.p=erExpression$pValues[,c("geneID","cID_7")],reference.p=tregBindingERalpha)
bindingExpressionConcordance[1:2]
## End. Not run
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