process_long_format: Long format to a wide format table using the MaxLFQ algorithm

In iq: Protein Quantification in Mass Spectrometry-Based Proteomics

Long format to a wide format table using the MaxLFQ algorithm

Description

A convenient function combining multiple steps to process a long format table using the MaxLFQ algorithm.

Usage

process_long_format(input_filename,
                    output_filename,
                    sample_id = "File.Name",
                    primary_id = "Protein.Group",
                    secondary_id = "Precursor.Id",
                    intensity_col = "Fragment.Quant.Corrected",
                    annotation_col = NULL,
                    filter_string_equal = NULL,
                    filter_string_not_equal = NULL,
                    filter_double_less = c("Q.Value" = "0.01", "PG.Q.Value" = "0.01"),
                    filter_double_greater = NULL,
                    intensity_col_sep = ";",
                    intensity_col_id = NULL,
                    na_string = "0",
                    normalization = "median",
                    log2_intensity_cutoff = 0,
                    pdf_out = "qc-plots.pdf",
                    pdf_width = 12,
                    pdf_height = 8,
                    show_boxplot = TRUE,
                    peptide_extractor = NULL)

Arguments

input_filename	See filename in fast_read.
output_filename	Output filename.
sample_id	See sample_id in fast_read.
primary_id	See primary_id in fast_read.
secondary_id	See secondary_id in fast_read.
intensity_col	See intensity_col in fast_read.
annotation_col	See annotation_col in fast_read.
filter_string_equal	See filter_string_equal in fast_read.
filter_string_not_equal	See filter_string_not_equal in fast_read.
filter_double_less	See filter_double_less in fast_read.
filter_double_greater	See filter_double_greater in fast_read.
intensity_col_sep	See intensity_col_sep in fast_read.
intensity_col_id	See intensity_col_id in fast_read.
na_string	See intensity_col_id in fast_read.
normalization	Normalization type. Possible values are median and none. The default value median is for median normalization in fast_preprocess.
log2_intensity_cutoff	See log2_intensity_cutoff in fast_preprocess.
pdf_out	See pdf_out in fast_preprocess.
pdf_width	See pdf_width in fast_preprocess.
pdf_height	See pdf_height in fast_preprocess.
show_boxplot	See show_boxplot in fast_preprocess.
peptide_extractor	A function to parse peptides.

Value

After processing with fast_read, fast_preprocess, and fast_MaxLFQ, the result table is written to output_filename. The quantification values are in log2 space. A NULL value is returned. If peptide_extractor is not NULL, fragment statistics for each protein will be calculated based on the result of the extractor function. Counting the number of peptides contributing to a protein is possible using an appropriate extractor function. An example value for peptide_extractor is function(x) gsub("[0-9].*$", "", x), which removes the charge state and fragment descriptors in an ion descriptor to obtain unique peptide sequences. One can examine the ion component returned by the fast_read function to derive a regular expression to be used in the gsub function above.

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.

See Also

fast_read, fast_preprocess, fast_MaxLFQ

iq documentation built on May 29, 2024, 8:40 a.m.