scDataConstructor: scData Constructor

In VCCRI/CIDR: Clustering through Imputation and Dimensionality Reduction

Description

scDataConstructor creates a new scData class object from a tag table.

Usage

scDataConstructor(tags, tagType = "raw")

Arguments

tags	a matrix of tags where the rows correspond to features (genes, transcripts, etc) and the columns correspond to cells.
tagType	- "raw" for when tags are raw counts ; "cpm" when tags are counts per million ; default is raw.

Details

Creates an object in scData (single-cell RNA-Seq dataset) class. Attributes of the class include scalar, vector and matrix data types necessary for the CIDR analysis - such as tag table, library sizes, dropout candidates, imputation weighting threshold. The tags can be raw counts (default) or counts per million (cpm). Raw counts are preferrable as the individual library sizes, as determined by the raw counts, are used to determine dropout candidates.

Value

an scData class object.

Examples

## Generate simulated single-cell RNA-Seq tags.
N=3 ## 3 cell types
k=50 ## 50 cells per cell type
sData <- scSimulator(N=N, k=k)
## The input for cidr should be a tag matrix.
## The default tagType is "raw" - meaning raw counts.
tags <- as.matrix(sData$tags)
## create a new scData object
sData <- scDataConstructor(tags)
## print the first 5 library sizes
sData@librarySizes[1:5]
## print a portion of the data matrix of the class - contains raw tags
sData@tags[1:5, 30:34]
## print part of the data matrix of the class - log tag per million
sData@nData[1:5, 30:34]

## Example on using tags that are counts per million (cpm)
## Note that we would only use cpm if we didn't have the raw counts.
tags_cpm <- t(t(tags)/colSums(tags))*1000000
## create a new scData object, specifying the tagType parameter
sData <- scDataConstructor(tags_cpm, tagType="cpm")
## print the first 5 library sizes
## Note that if only the cpm data is available, we do not know the 
## library sizes.  In this case CIDR sets all the library sizes to
## 1 million.
sData@librarySizes[1:5]
## print a portion of the data matrix of the class - contains raw tags
sData@tags[1:5, 30:34]
## print part of the data matrix of the class - log tag per million
sData@nData[1:5, 30:34]

VCCRI/CIDR documentation built on May 9, 2019, 9:41 p.m.