guess_maxquant_quantity {autonomics}

R Documentation

Guess maxquant quantity from snames

Description

character vector, dataframe, or SummarizedExperiment.

Usage

guess_maxquant_quantity(x, ...)

## S3 method for class 'character'
guess_maxquant_quantity(x, ...)

## S3 method for class 'data.frame'
guess_maxquant_quantity(x, ...)

## S3 method for class 'SummarizedExperiment'
guess_maxquant_quantity(x, ...)

Arguments

x	character vector, dataframe, or SummarizedExperiment
...	used for proper S3 method dispatch

Value

string: value from names(MAXQUANT_PATTERNS_QUANTITY)

Examples

# file
    file <- download_data('fukuda20.proteingroups.txt')
    guess_maxquant_quantity(file)

# character vector
    x <- "Ratio M/L normalized STD(L)_E00(M)_E01(H)_R1"
    guess_maxquant_quantity(x)

    x <- "Ratio M/L STD(L)_E00(M)_E01(H)_R1"
    guess_maxquant_quantity(x)

    x <- "LFQ intensity E00.R1"
    guess_maxquant_quantity(x)

    x <- "Reporter intensity corrected 0 STD(0)E00(1)E01(2)_R1"
    guess_maxquant_quantity(x)

    x <- "Reporter intensity 0 STD(0)E00(1)E01(2)_R1"
    guess_maxquant_quantity(x)

    x <- "Intensity H STD(L)_E00(M)_E01(H)_R1"
    guess_maxquant_quantity(x)

# dataframe
    file <- download_data('fukuda20.proteingroups.txt')
    x <- data.table::fread(file)
    guess_maxquant_quantity(x)

# SummarizedExperiment
    file <- download_data('fukuda20.proteingroups.txt')
    object <- read_proteingroups(file, plot=FALSE)
    guess_maxquant_quantity(file)

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