process_long_format | R Documentation |
A convenient function combining multiple steps to process a long format table using the MaxLFQ algorithm.
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)
input_filename |
See |
output_filename |
Output filename. |
sample_id |
See |
primary_id |
See |
secondary_id |
See |
intensity_col |
See |
annotation_col |
See |
filter_string_equal |
See |
filter_string_not_equal |
See |
filter_double_less |
See |
filter_double_greater |
See |
intensity_col_sep |
See |
intensity_col_id |
See |
na_string |
See |
normalization |
Normalization type. Possible values are |
log2_intensity_cutoff |
See |
pdf_out |
See |
pdf_width |
See |
pdf_height |
See |
show_boxplot |
See |
peptide_extractor |
A function to parse peptides. |
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.
Thang V. Pham
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.
fast_read
, fast_preprocess
, fast_MaxLFQ
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