View source: R/Script_PLATE_08_DE_5_1_IsoSwitch.R
IsoSwitch | R Documentation |
Classify gene-splicing relative changes to each other from cell group 1 to group 2. Classifications are coordinated, opposing, isoform-switching, and complex. In coordinated relationship, both gene and splicing changes in the same direction from cell group 1 to group 2. In opposing relationship, gene changes in the opposite direction relative to splicing from cell group 1 to group 2. In isoform-switching, there is differential splice junction usage without differential expression of the corresponding gene between cell group 1 and group 2. Complex relationship involves genes with both coordinated and opposing relationships with splicing. Only differentially spliced junctions are included for analysis here.
IsoSwitch( MarvelObject, method, psi.pval = 0.1, psi.delta = 0, gene.pval = 0.1, gene.log2fc = 0.5, event.type = NULL, custom.tran_ids = NULL )
MarvelObject |
Marvel object. S3 object generated from |
method |
Character string. The statistical method used for differential splicing analysis. |
psi.pval |
Numeric value. Adjusted p-value below which the splicing event is considered differentially spliced and included for isoform switching analysis. To be used in conjunction with |
psi.delta |
Numeric value. The absolute mininum difference in PSI values between the two cell groups above which the splicing event is considered differentially spliced nd included for isoform switching analysis. To be used in conjunction with |
gene.pval |
Numeric value. Adjusted p-value below which the gene is considered differentially expressed. Default value is |
gene.log2fc |
Numeric value. The absolute log2 fold change in mean gene expression values between the two cell groups above which the gene is considered differentially expressed. To be used in conjunction with |
event.type |
Character string. Indicate which splicing event type to include for analysis. Can take any combination of values: |
custom.tran_ids |
Vector of character strings. Subset of tran_ids to be brought forward for analysis after filtering based on |
An object of class S3 containing with new slots MarvelObject$DE$Cor$Table
, MarvelObject$DE$Cor$Plot
, and MarvelObject$DE$Cor$Plot.Stats
.
marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL")) marvel.demo <- IsoSwitch(MarvelObject=marvel.demo, method="ad", psi.pval=0.1, psi.delta=0, gene.pval=0.1, gene.log2fc=0.5 ) # Check outputs head(marvel.demo$DE$Cor$Table_Raw) head(marvel.demo$DE$Cor$Table) marvel.demo$DE$Cor$Plot marvel.demo$DE$Cor$Plot.Stats
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.