new_scGPS_object {scGPS} | R Documentation

## new_scGPS_object

### Description

`new_scGPS_object` generates a scGPS object in the SingleCellExperiment class for use with the scGPS package. This object contains an expression matrix, associated metadata (cells, genes, clusters). The data are expected to be normalised counts.

### Usage

    new_scGPS_object(
      ExpressionMatrix = NULL,
      GeneMetadata = NULL,
      CellMetadata = NULL,
      LogMatrix = NULL
    )

### Arguments

`ExpressionMatrix` | An expression matrix in data.frame or matrix format. Rows should represent a transcript and its normalised counts, while columns should represent individual cells.
`GeneMetadata` | A data frame or vector containing gene identifiers used in the expression matrix. The first column should hold the gene identifiers you are using in the expression matrix. Other columns contain information about the genes, such as their corresponding ENSEMBL transcript identifiers.
`CellMetadata` | A data frame containing cell identifiers (usually barcodes) and an integer representing which batch they belong to. The column containing clustering information needs to be the first column in the CellMetadata dataframe If clustering information is not available, users can run CORE function and add the information to the scGPS before running scGPS prediction
`LogMatrix` | optional input for a log matrix of the data. If no log matrix is supplied one will be created for the object

### Value

This function generates an scGPS object belonging to the SingleCellExperiment.

### Author(s)

Quan Nguyen, 2018-04-06

### See Also

SingleCellExperiment

### Examples

    day2 <- day_2_cardio_cell_sample
    t <-new_scGPS_object(ExpressionMatrix = day2$dat2_counts,
        GeneMetadata = day2$dat2geneInfo, CellMetadata = day2$dat2_clusters)
    colData(t); show(t); colnames(t)

[Package scGPS version 1.8.0 Index]