AssignModality: Assign modalities

In MARVEL: Revealing Splicing Dynamics at Single-Cell Resolution

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
)

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.

Value

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

Author(s)

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)

MARVEL documentation built on Oct. 31, 2022, 5:07 p.m.