MARVEL (version 1.4.0)

AssignModality: Assign modalities

Description

Assigns modalities to each splicing event for a specified group of cells.

Usage

AssignModality(
  MarvelObject,
  sample.ids,
  min.cells = 25,
  sigma.sq = 0.001,
  bimodal.adjust = TRUE,
  bimodal.adjust.fc = 3,
  bimodal.adjust.diff = 50,
  seed = 1,
  tran_ids = NULL
)

Value

An object of class S3 containing with new slot MarvelObject$Modality$Results.

Arguments

MarvelObject

Marvel object. S3 object generated from TransformExpValues function.

sample.ids

Vector of character strings. Sample IDs that constitute the cell group.

min.cells

Numeric value. The minimum no. of cells expressing the splicing event for the event to be included for modality assignment.

sigma.sq

Numeric value. The variance threshold below which the included/excluded modality will be defined as primary sub-modality, and above which it will be defined as dispersed sub-modality.

bimodal.adjust

Logical. When set to TRUE, MARVEL will identify false bimodal modalities and reassign them as included/excluded modality.

bimodal.adjust.fc

Numeric value. The ratio between the proportion of cells with >0.75 PSI vs <0.25 PSI (and vice versa) below which the splicing event will be classified as bimodal. Only applicable when bimodal.adjust set to TRUE. To be used in conjunction with bimodal.adjust.diff.

bimodal.adjust.diff

Numeric value. The difference between the percentage of cells with >0.75 PSI vs <0.25 PSI (and vice versa) below which the splicing event will be classified as bimodal. Only applicable when bimodal.adjust set to TRUE. To be used in conjunction with bimodal.adjust.fc.

seed

Numeric value. Ensure the fitdist function returns the same values for alpha and beta paramters each time this function is executed using the same random number generator.

tran_ids

Character strings. Specific vector of transcript IDs for modality assignment. This will be a subset of all transcripts expressed in sufficient number of cells as defined in min.cells option.

Author

Sean Wen <[e-mail]>

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

df.pheno <- marvel.demo$SplicePheno
sample.ids <- df.pheno[which(df.pheno$cell.type=="iPSC"), "sample.id"]

# Assign modality
marvel.demo <- AssignModality(MarvelObject=marvel.demo,
                              sample.ids=sample.ids,
                              min.cells=5
                              )

# Check output
head(marvel.demo$Modality$Results)