Protein_Domain_Enrichment: Protein_Domain_Enrichment

In jpromeror/EventPointer: An effective identification of alternative splicing events using junction arrays and RNA-Seq data

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

## Not run: 
   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)
   
## End(Not run)

jpromeror/EventPointer documentation built on May 17, 2023, 10:29 p.m.