.read_maxquant {autonomics} | R Documentation |
Read/Analyze proteingroups/phosphosites
.read_maxquant( file, quantity = guess_maxquant_quantity(file), sfile = NULL, sfileby = NULL, subgroupvar = "subgroup", select_subgroups = NULL, invert_subgroups = character(0), pepcountpattern = MAXQUANT_PATTERNS_PEPCOUNTS[1], verbose = TRUE ) read_proteingroups( file, quantity = guess_maxquant_quantity(file), sfile = NULL, sfileby = NULL, select_subgroups = NULL, contaminants = FALSE, reverse = FALSE, fastafile = NULL, invert_subgroups = character(0), impute = stri_detect_regex(quantity, "[Ii]ntensity"), pepcountpattern = MAXQUANT_PATTERNS_PEPCOUNTS[1], subgroupvar = NULL, formula = NULL, block = NULL, contrastdefs = NULL, pca = FALSE, fit = NULL, verbose = TRUE, plot = TRUE ) read_phosphosites( file, proteinfile = paste0(dirname(file), "/proteinGroups.txt"), quantity = guess_maxquant_quantity(file), sfile = NULL, sfileby = NULL, select_subgroups = NULL, contaminants = FALSE, reverse = FALSE, min_localization_prob = 0.75, fastafile = NULL, invert_subgroups = character(0), pca = FALSE, fit = NULL, subgroupvar = NULL, formula = NULL, block = NULL, contrastdefs = NULL, verbose = TRUE, plot = TRUE )
file |
proteingroups/phosphosites file |
quantity |
string: "Ratio normalized", "Ratio", "LFQ intensity", "Reporter intensity corrected", "Reporter intensity", "Intensity labeled", "Intensity" |
sfile |
sample file |
sfileby |
sample file mergeby column |
subgroupvar |
subgroup svar |
select_subgroups |
subgroups to be selected (character vector) |
invert_subgroups |
subgroups to be inverted (character vector) |
pepcountpattern |
value in MAXQUANT_PATTERNS_PEPCOUNTS |
verbose |
whether to message |
contaminants |
whether to return contaminants |
reverse |
whether to return reverse peptides |
fastafile |
NULL or fastafile (to deconvolute proteingroups) |
impute |
whether to impute consistent nondetects |
formula |
desgnmat formula |
block |
block svar |
contrastdefs |
contrastdef vector/matrix/list |
pca |
whether to pca |
fit |
fit model: NULL, 'limma', 'lm', 'lme', 'lmer','wilcoxon' |
plot |
whether to plot |
proteinfile |
proteingroups file |
min_localization_prob |
min site localization probability (number) |
SummarizedExperiment
file <- download_data('fukuda20.proteingroups.txt') object <- read_proteingroups(file, pca=TRUE, fit='limma')