Protein_Domain_Enrichment {EventPointer} | R Documentation

## Protein_Domain_Enrichment

### Description

Analyze whether the presence of a protein domain increases or decreases in the condition under study.

### Usage

    Protein_Domain_Enrichment(PathsxTranscript, TxD, Diff_PSI, method = "spearman")

### Arguments

`PathsxTranscript` | the output of EventDetection_transcriptome.
`TxD` | matrix that relates transcripts with Protein domain. Users can get it from BioMart
`Diff_PSI` | matrix with the difference of psi of the condition under study. Can get it from the output of EventPointer_Bootstraps
`method` | a character string indicating which correlation coeffcient is to be calculated. "spearman" (default) or "pearson" can be selected.

### Value

A list containing the results of the protein domain enrichment anaylisis. This list contains 3 matrices in which the rows indicate the protein domains and the columns the number of contrasts. The 3 matrices are the following:

-mycor: correlation value between the deltaPSI and the DifProtDomain matrix (see more details in vignette)

-STATISTIC: the values of the test statistic

-PVAL: the pvalues of the test statistic

### Examples

       data("EventXtrans")
       data("TxD")
       data("Fit")

       #same annotation in TxD and EventXtrans
       transcriptnames <- EventXtrans$transcritnames
       transcriptnames <- gsub("\\..*","",transcriptnames)
       EventXtrans$transcritnames <- transcriptnames

       Result_PDEA <- Protein_Domain_Enrichment(PathsxTranscript = EventXtrans,
                                                TxD = TxD,
                                                Diff_PSI = Fit$deltaPSI)

[Package EventPointer version 3.2.0 Index]