geva.input.correct {geva} | R Documentation

## GEVA Input Post-processing

### Description

Helper functions used to edit the contents from a `GEVAInput`.

### Usage

    geva.input.correct(ginput, na.rm = TRUE, inf.rm = TRUE, invalid.col.rm = TRUE)

    geva.input.filter(
      ginput,
      p.value.cutoff = 0.05,
      by.any = FALSE,
      na.val = 0,
      ...
    )

    geva.input.rename.rows(
      ginput,
      attr.column,
      dupl.rm.method = c("least.p.vals", "order")
    )

### Arguments

`ginput` | A `GEVAInput` object
`na.rm` | `logical`; if `TRUE`, removes all rows containing `NA`
`inf.rm` | `logical`; if `TRUE`, removes all rows containing infinite values (`Inf` or `-Inf`)
`invalid.col.rm` | `logical`; if `TRUE`, searches for any column that is entirely composed by invalid values (according to the other arguments) and removes it before checking the rows
`p.value.cutoff` | `numeric` (`0` to `1`), the p-value cutoff. Rows containing values above this threshold are removed
`by.any` | `logical`, set to `TRUE` to delete the rows with at least one occurrence above the cutoff; or `FALSE` to delete only those rows in which all values are above the specified threshold
`na.val` | `numeric`, the replacement for `NA` values
`...` | optional arguments. Accepts `verbose` (`logical`, default is `TRUE`) to enable or disable printing the progress
`attr.column` | `character`, target column with the values that will replace the current row names
`dupl.rm.method` | `character`, method to remove duplicate names. The possible options are: `"least.p.vals"` : Keeps the duplicate that contains the least sum of p-values `"order"` : Keeps the first occurrence of the duplicate in the current row order

### Details

`geva.input.correct` corrects the numeric input data (values and weights), removing rows that include invalid values such as NA or infinite.

`geva.input.filter` attempts to select the most relevant part of the input data, removing rows containing p.values (1 - weights) above a specific threshold.

`geva.input.rename.rows` replaces the row names with a column from the feature table (see `GEVAInput`). The column name specified for `attr.column` must be included in the `names(featureTable(ginput))`. Any duplicates are removed according to the `dupl.rm.method`, and the selected duplicates are stored as a new column named `"renamed_id"` inside the feature table from the returned object.

### Value

A modified `GEVAInput` object

### Examples

    ## geva.input.correct example
    colexample1 <- runif(1000, -1, 1)        # Random column 1
    colexample2 <- runif(1000, -1, 1)        # Random column 2
    colexample3 <- runif(1000, -1, 1)        # Random column 3
    colexample3[runif(1000, -1, 1) < 0] = NA # Random NA's
    ginput = geva.merge.input(col1=colexample1,
                              col2=colexample2,
                              col3=colexample3)
    # Before the correction:
    print(nrow(ginput))    # Returns 1000
    # Applies the correction (removes rows with NA's)
    ginput <- geva.input.correct(ginput)
    # After the correction:
    print(nrow(ginput))    # Returns less than 1000

    ## ---
    ## geva.input.filter example
    ginput <- geva.ideal.example(1000)  # Generates a random input
    # Before the filter:
    print(nrow(ginput))    # Returns 1000
    # Applies the filter
    ginput <- geva.input.filter(ginput)
    # After the filter:
    print(nrow(ginput))    # Returns less than 1000

    ## ---
    ## geva.input.rename.rows example
    ginput <- geva.ideal.example()  # Generates a random input
    # Renames to 'Symbol'
    ginput <- geva.input.rename.rows(ginput,
                                     attr.column = "Symbol")
    print(head(ginput))             # The row names are set now as the gene symbols

[Package geva version 1.0.0 Index]