msSummarize {MSPrep} | R Documentation

## Function for summarizing technical replicates.

### Description

Reads data and summarizes technical replicates as the mean of observations for compounds found in 2 or 3 replicates and with coefficient of variation below specified level, or median for those found in 3 replicates but with excessive coefficient of variation (CV). Compounds found in only 1 replicate are assigned as missing.

### Usage

    msSummarize(
      data,
      cvMax = 0.5,
      minPropPresent = 1/3,
      replicate = "replicate",
      compVars = c("mz", "rt"),
      sampleVars = c("subject_id"),
      colExtraText = NULL,
      separator = NULL,
      missingValue = NA,
      returnSummaryDetails = FALSE,
      returnToSE = FALSE,
      returnToDF = FALSE
    )

### Arguments

`data` | Data set as either a data frame or 'SummarizedExperiement'.
`cvMax` | Decimal value from 0 to 1 representing the acceptable level of coefficient of variation between replicates.
`minPropPresent` | Decimal value from 0 to 1 representing the minimum proportion present to summarize with median or mean. Below this the compound will be set to 0.
`replicate` | Name of sample variable specifying replicate. Must match an element in 'sampleVars' or a column in the column data of a 'SummarizedExperiment'.
`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'.
`returnSummaryDetails` | Logical value specifying whether to return details of replicate summarization.
`returnToSE` | Logical value specifying whether to return as 'SummarizedExperiment'
`returnToDF` | Logical value specifying whether to return as data frame.

### Value

A data frame or 'SummarizedExperiment' containing abundance data with summarized technical replicates. Default return type is set to match the data nput but may be altered with the 'returnToSE' or 'returnToDF' arguments. If 'returnSummaryDetails' is selected, a list will be returned containing the summarized data and a separate tidy data frame with summarization details included for each compound/sample pair.

### Examples

    # Read in data file
    data(msquant)

    # Summarize technical replicates
    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)

[Package MSPrep version 1.0.0 Index]