buildAltSpliceIndex: Builds an 'SCFind' object from a 'matrix'

In YY-SONG0718/scfindME: This is a package that adaps "scfind", a search tool for single cell RNA-seq data by gene lists, to alternative splicing analysis

Builds an SCFind object from a matrix

Description

This function will index a matrix including alternative splicing information for each cell as an SCFind index.

Usage

buildAltSpliceIndex.PSI(psival, metadata, dataset.name, column.label, qb = 2)

## S4 method for signature 'ANY'
buildAltSpliceIndex(
  psival,
  metadata,
  dataset.name,
  column.label = "primary_type",
  qb = 2
)

Arguments

psival	a dataframe object containing psi value of each node of a gene and cell with gene_node as row.names and cell id as col.names
metadata	metadata of the alternative splicing dataset, must include cell.type information for the dataset
dataset.name	name of the dataset, i.e. tissue name
column.label	the cell.type in metadata that will be used for the index
qb	number of bits per cell that are going to be used for quantile compression of the expression data

Value

an SCFind object

YY-SONG0718/scfindME documentation built on April 17, 2023, 4:27 a.m.