mdgsa (version 1.4.2)

transferIndex: Transfer a ranking index from regulatory elements, such as miRNAs, to genes.

Description

Transfers the ranking index information from some regulatory elements to their target genes. It can be for instance used to infer gene regulation levels from miRNA differential expression levels. Afterwords, the inferred gene index can be explored in a univariate gene set analysis using uvGsa, or in a multivariate gene set analysis using mdGsa.

Usage

transferIndex(index, targets, method = "sum", verbose = TRUE,
  transferMatrix = FALSE)

Arguments

index

ranking index, generally a numerical named vector.

targets

a list describing the regulation blocks. See details.

method

the method to collapse the gene information. Currently 'sum' and 'average' are available.

verbose

verbose.

transferMatrix

if true the transference matrix is returned instead of the ranking statistic.

Value

• A ranking index transferred to the IDs in the elements of the list targets.

Details

The function was in principle designed to transfer a ranking index defined for miRNAs to their target genes, but it may also be used to deal with some other regulatory elements as transcription factors for instance.

If we have for instance a t statistic accounting for miRNAs differential expression levels, we may add up (or average) all t values from the miRNAs that regulate a gene in order to derive an interference score for that gene. Thus we may get an interference index which may be interpreted in terms of functional blocks or gene sets.

index may be a matrix. In such case just the first column will be used.

targets should be a named list. The names of the list have to coincide (or at least overlap) with the names in the index. The elements of the list are character vectors containing gene IDs. In the miRNA example, each element of targets will contain the genes regulated by a miRNA, and the miRNA IDs will appear in the names of the targets list as well as in the ranking index.

See Also

uvGsa, mdGsa, indexTransform

Examples

## miRNA to gene list (targets)
targets <- list (mirna1 = "g1", mirna2 = c ("g1", "g2"), mirna3 = "g3")

## original index
index <- rnorm (5)
names (index) <- paste0 ("mirna", 1:5)

##transfered index
tindex <- transferIndex (index, targets)

##transformed (normalized) index
rindex <- indexTransform (tindex)

##NOTICE in this case:
index["mirna1"] + index["mirna2"] == tindex["g1"]

res <- uvgsa (rindex, annot)