create_protein_table | R Documentation |
Travels through the input list and quantifies all proteins one by one.
create_protein_table(protein_list, method = "maxLFQ", ...)
protein_list |
The input protein list |
method |
Possible values are "maxLFQ", "median_polish", "topN", and "meanInt". |
... |
Additional parameters for individual quantitation methods. |
A list of two components is returned
estimate |
A table of protein abundances for all samples in log2 space. |
annotation |
A vector of annotations, one for each protein. |
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.
create_protein_list
, maxLFQ
, median_polish
, topN
, meanInt
data("spikeins")
# This example set of spike-in proteins has been 'median-normalized'.
norm_data <- iq::preprocess(spikeins, median_normalization = FALSE, pdf_out = NULL)
protein_list <- iq::create_protein_list(norm_data)
result <- iq::create_protein_table(protein_list)
head(result)
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