msSummarize: Function for summarizing technical replicates.

In KechrisLab/MSPrep: Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data

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)
                            

KechrisLab/MSPrep documentation built on Feb. 2, 2022, 2:43 a.m.