msFilter {MSPrep} | R Documentation

## Function for filtering abundance data set.

### Description

Filters compounds to those found in specified proportion of samples.

### Usage

    msFilter(
      data,
      filterPercent = 0.8,
      compVars = c("mz", "rt"),
      sampleVars = c("subject_id"),
      colExtraText = NULL,
      separator = NULL,
      missingValue = NA,
      returnToSE = FALSE,
      returnToDF = FALSE
    )

### Arguments

`data` | Data set as either a data frame or 'SummarizedExperiement'.
`filterPercent` | Decimal value indicating filtration threshold. Compounds which are present in fewer samples than the specified proportion will be removed.
`compVars` | Vector of the columns which identify compounds. If a 'SummarizedExperiment' is used for 'data', row variables will be used.
`sampleVars` | Vector of the ordered sample variables found in each sample column.
`colExtraText` | Any extra text to ignore at the beginning of the sample columns names. Unused for 'SummarizedExperiments'.
`separator` | Character or text separating each sample variable in sample columns. Unused for 'SummarizedExperiment'.
`missingValue` | Specifies the abundance value which indicates missing data. May be a numeric or 'NA'.
`returnToSE` | Logical value indicating whether to return as 'SummarizedExperiment'
`returnToDF` | Logical value indicating whether to return as data frame.

### Value

A data frame or 'SummarizedExperiment' with filtered abundance data. Default return type is set to match the data input but may be altered with the 'returnToSE' or 'returnToDF' arguments.

### Examples

    # Load example data set, summarize replicates
    data(msquant)

    summarizedDF <- msSummarize(msquant,
                                compVars = c("mz", "rt"),
                                sampleVars = c("spike", "batch", "replicate",
                                "subject_id"),
                                cvMax = 0.50,
                                minPropPresent = 1/3,
                                colExtraText = "Neutral_Operator_Dif_Pos_",
                                separator = "_",
                                missingValue = 1)

    # Filter the dataset using a 80% filter rate
    filteredDF <- msFilter(summarizedDF,
                           filterPercent = 0.8,
                           compVars = c("mz", "rt"),
                           sampleVars = c("spike", "batch", "subject_id"),
                           separator = "_")

[Package MSPrep version 1.0.0 Index]