TransposeAssay {pathwayPCA} | R Documentation

## Transpose an Assay (Data Frame)

### Description

Transpose an object of class `data.frame` that contains assay measurements while preserving row (feature) and column (sample) names.

### Usage

    TransposeAssay(
      assay_df,
      omeNames = c("firstCol", "rowNames"),
      stringsAsFactors = FALSE
    )

### Arguments

`assay_df` | A data frame with numeric values to transpose
`omeNames` | Are the data feature names in the first column or in the row names of `df`? Defaults to the first column. If the feature names are in the row names, this function assumes that these names are accesible by the `rownames` function called on `df`.
`stringsAsFactors` | Should columns containing string information be coerced to factors? Defaults to `FALSE`.

### Details

This function is designed to transpose "tall" assay data frames (where genes or proteins are the rows and patient or tumour samples are the columns). This function also transposes the row (feature) names to column names and the column (sample) names to row names. Notice that all rows and columns (other than the feature name column, as applicable) are numeric.

Recall that data frames require that all elements of a single column to have the same `class`. Therefore, sample IDs of a "tall" data frame must be stored as the column names rather than in the first row.

### Value

The transposition of `df`, with row and column names preserved and reversed.

### Examples

       x_mat <- matrix(rnorm(5000), ncol = 20, nrow = 250)
       rownames(x_mat) <- paste0("gene_", 1:250)
       colnames(x_mat) <- paste0("sample_", 1:20)
       x_df <- as.data.frame(x_mat, row.names = rownames(x_mat))

       TransposeAssay(x_df, omeNames = "rowNames")

[Package pathwayPCA version 1.10.0 Index]