preprocess: Data preprocessing for protein quantification

In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

Data preprocessing for protein quantification

Description

Prepares a long-format input including removing low-intensity ions and performing median normalization.

Usage

preprocess(quant_table,
           primary_id = "PG.ProteinGroups",
           secondary_id = c("EG.ModifiedSequence", "FG.Charge", "F.FrgIon", "F.Charge"),
           sample_id = "R.Condition",
           intensity_col = "F.PeakArea",
           median_normalization = TRUE,
           log2_intensity_cutoff = 0,
           pdf_out = "qc-plots.pdf",
           pdf_width = 12,
           pdf_height = 8,
           intensity_col_sep = NULL,
           intensity_col_id = NULL,
           na_string = "0")

Arguments

quant_table	A long-format table with a primary column of protein identification, secondary columns of fragment ions, a column of sample names, and a column for quantitative intensities.
primary_id	Unique values in this column form the list of proteins to be quantified.
secondary_id	A concatenation of these columns determines the fragment ions used for quantification.
sample_id	Unique values in this column form the list of samples.
intensity_col	The column for intensities.
median_normalization	A logical value. The default TRUE value is to perform median normalization.
log2_intensity_cutoff	Entries lower than this value in log2 space are ignored. Plot a histogram of all intensities to set this parameter.
pdf_out	A character string specifying the name of the PDF output. A NULL value will suppress the PDF output.
pdf_width	Width of the pdf output in inches.
pdf_height	Height of the pdf output in inches.
intensity_col_sep	A separator character when entries in the intensity column contain multiple values.
intensity_col_id	The column for identities of multiple quantitative values.
na_string	The value considered as NA.

Details

When entries in the intensity column contain multiple values, this function will replicate entries in other column and the secondary_id will be appended with corresponding entries in intensity_col_id when it is provided. Otherwise, integer values 1, 2, 3, etc... will be used.

Value

A data frame is returned with following components

protein_list	A vector of proteins.
sample_list	A vector of samples.
id	A vector of fragment ions to be used for quantification.
quant	A vector of log2 intensities.

Author(s)

Thang V. Pham

References

Pham TV, Henneman AA, Jimenez CR. iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics. Bioinformatics 2020 Apr 15;36(8):2611-2613.

Examples

data("spikeins")
head(spikeins)
# This example set of spike-in proteins has been 'median-normalized'.
norm_data <- iq::preprocess(spikeins, median_normalization = FALSE, pdf_out = NULL)

iq documentation built on March 31, 2023, 11:34 p.m.