loadDataOrMatrix {conclus} | R Documentation

## loadDataOrMatrix

### Description

This function allows to import the coldata, rowData or the countMatrix. It formats each type of data to follow the requirements of CONCLUS.

### Usage

    loadDataOrMatrix(file, type, columnID=NULL, header=TRUE, sep='\t', dec=".",
                        ignoreCellNumber=FALSE)

### Arguments

`file` | Path to the rowData, colData or Matrix.
`type` | Values should be "coldata", "rowdata", or "countMatrix".
`columnID` | For row and col data, column name containing cells/genes names/id. Should be the same names of genes or cells that in the count matrix. Should not be used when importing a matrix. Default=NULL.
`header` | Set TRUE if the first row of the table corresponds to the column names, and FALSE if it doesn't. Default=TRUE.
`sep` | Character used in the table to separate the fields. Usually it's ' ' ';' ',' or '\t'. Default='\t'.
`dec` | Character used in the table for decimal points. Usually '.' or ',' . Default=".".
`ignoreCellNumber` | CONCLUS needs a large number of cells to collect statistics, so we recommend using CONCLUS if you have at least 100 cells. If you still want to use a count matrix with a number of cells inferior to 100 cells, set ignoreCellNumber=TRUE. Default=FALSE.

### Value

The formatted row, col data or the matrix.

### Author(s)

Ilyess RACHEDI and Nicolas DESCOSTES

### Examples

    ## ColData
    coldataPath <- system.file("extdata/colData.tsv", package="conclus")
    loadDataOrMatrix(file=coldataPath, type="coldata", columnID="cell_ID")

    ## RowData
    rowdataPath <- system.file("extdata/rowData.tsv",  package="conclus")
    loadDataOrMatrix(file=rowdataPath, type="rowdata", columnID="gene_ID")

    ## Count matrix
    countmatrixPath <- system.file("extdata/countMatrix.tsv", package="conclus")
    countMatrix <- loadDataOrMatrix(file=countmatrixPath, type="countMatrix",
                                    ignoreCellNumber=TRUE)

[Package conclus version 1.2.4 Index]