getStatistics {benchdamic} | R Documentation

## getStatistics

### Description

Extract the list of p-values or/and log fold changes from the output of a differential abundance detection method.

### Usage

    getStatistics(
      method,
      slot = "pValMat",
      colName = "rawP",
      type = "pvalue",
      direction = NULL,
      verbose = FALSE
    )

### Arguments

`method` | Output of a differential abundance detection method. `pValMat`, `statInfo` matrices, and method's `name` must be present (See vignette for detailed information).
`slot` | The slot name where to extract values (default `slot = "pValMat"`).
`colName` | The column name of the slot where to extract values (default `colName = "rawP"`).
`type` | The value type of the column selected where to extract values. Two values are possible: `"pvalue"` or `"logfc"` (default `type = "pvalue"`).
`direction` | `statInfo`'s column name containing information about the signs of differential abundance (usually log fold changes) (default `direction = NULL`).
`verbose` | Boolean to display the kind of extracted values (default `verbose = FALSE`).

### Value

A vector or a `data.frame`. If `direction = NULL`, the `colname` column values, transformed according to `type` (not tranformed if `type = "pvalue"`, `-abs(value)` if `type = "logfc"`), of the `slot` are reported, otherwise the `direction` column of the `statInfo` matrix is added to the output.

### See Also

`extractStatistics`

### Examples

    data("ps_plaque_16S")
    # Add scaling factors
    ps_plaque_16S <- norm_edgeR(object = ps_plaque_16S, method = "TMM")
    # DA analysis
    da.limma <- DA_limma(
        object = ps_plaque_16S,
        design = ~ 1 + HMP_BODY_SUBSITE,
        coef = 2,
        norm = "TMM"
    )
    # get p-values
    getStatistics(
        method = da.limma, slot = "pValMat", colName = "rawP",
        type = "pvalue", direction = NULL
    )
    # get negative abs(logFC) values
    getStatistics(
        method = da.limma, slot = "statInfo", colName = "logFC",
        type = "logfc", direction = NULL
    )
    # get p-values and logFC
    getStatistics(
        method = da.limma, slot = "pValMat", colName = "rawP",
        type = "pvalue", direction = "logFC"
    )

[Package benchdamic version 1.0.0 Index]