Filters out low intensities and performs median normalization.
fast_preprocess(quant_table,
median_normalization = TRUE,
log2_intensity_cutoff = 0,
pdf_out = "qc-plots-fast.pdf",
pdf_width = 12,
pdf_height = 8,
show_boxplot = TRUE)A list is returned with the same components as input data in which low intensities are filtered out and median normalization is performed if requested.
The quant_table component as returned by fast_read.
A logical value. The default TRUE value is to perform median normalization.
Entries lower than this value in log2 space are ignored. Plot a histogram of all intensities to set this parameter.
A character string specifying the name of the PDF output. A NULL value will suppress the PDF output.
Width of the pdf output in inches.
Height of the pdf output in inches.
A logical value. The default TRUE value is to create boxplots of fragment intensities for each sample.
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