long_format_to_iq_format: Long format input data to iq format

Description

This function reads long-format input data, filters it, and writes the results to the iq format.

Usage

long_format_to_iq_format(input_data, 
                         output_data,
                         sample_id = "Run",
                         primary_id = "Protein.Group",
                         secondary_id = c("Precursor.Id"),
                         intensity_col = "Intensities",
                         annotation_col = NULL,
                         filter_string_equal = NULL,
                         filter_string_not_equal = NULL,
                         filter_double_less = NULL,
                         filter_double_greater = NULL,
                         intensity_col_sep = ";",
                         intensity_col_id = NULL, 
                         na_string = "0",
                         normalization = "median",
                         log2_intensity_cutoff = 0,
                         pdf_out = "qc-plots-iq.pdf",
                         pdf_width = 12,
                         pdf_height = 8,
                         show_boxplot = FALSE)

Value

The output is written to a new directory named output_data.

Arguments

input_data: See filename in fast_read.
output_data: Output data.
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.

Author

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.

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