read_diann_proteingroups: Read diann

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Read diann

Description

Read diann

Usage

.read_diann_precursors(file, Lib.PG.Q = 0.01, verbose = TRUE)

.read_diann_proteingroups(file, Lib.PG.Q = 0.01)

read_diann_proteingroups(
  file,
  Lib.PG.Q = 0.01,
  simplify_snames = TRUE,
  contaminants = character(0),
  impute = FALSE,
  plot = FALSE,
  pca = plot,
  pls = plot,
  fit = if (plot) "limma" else NULL,
  formula = as.formula("~ subgroup"),
  block = NULL,
  coefs = NULL,
  contrasts = NULL,
  palette = NULL,
  verbose = TRUE
)

read_diann(...)

Arguments

file	'report.tsv' file
Lib.PG.Q	Lib.PG.Q cutoff
verbose	TRUE or FALSE
simplify_snames	TRUE or FALSE: simplify (drop common parts in) samplenames ?
contaminants	character vector: contaminant uniprots
impute	TRUE or FALSE: impute group-specific NA values?
plot	TRUE or FALSE
pca	TRUE or FALSE: run pca ?
pls	TRUE or FALSE: run pls ?
fit	model engine: 'limma', 'lm', 'lme(r)', 'wilcoxon' or NULL
formula	model formula
block	model blockvar: string or NULL
coefs	model coefficients of interest: character vector or NULL
contrasts	coefficient contrasts of interest: character vector or NULL
palette	color palette: named string vector
...	used to maintain deprecated functions

Value

data.table or SummarizedExperiment

Examples

# Read
   file <- download_data('dilution.report.tsv')
   .read_diann_precursors(file)         #    precursors longdt
   .read_diann_proteingroups(file)      # proteingroups longdt
   fdt(read_diann_proteingroups(file))  # proteingroups sumexp
# Compare
    PR <- .read_diann_precursors(file)
    PG <- .read_diann_proteingroups(file)
    PG[intensity==top1] # matches      : 24975 (85%) proteingroups
    PG[intensity!=top1] # doesnt match :  4531 (15%) proteingroups
    RUN <- 'IPT_HeLa_1_DIAstd_Slot1-40_1_9997'
    PR[uniprot=='Q96JP5;Q96JP5-2' & run == RUN, 1:6] #    match:    8884 ==   8884
    PR[uniprot=='P36578'          & run == RUN, 1:6] # no match:  650887 != 407978
    PR[intensity != top1][feature_id == unique(feature_id)[1]][run == unique(run)[1]][1:2, 1:6]
    PR[intensity != top1][feature_id == unique(feature_id)[2]][run == unique(run)[1]][1:2, 1:6]
    PR[intensity != top1][feature_id == unique(feature_id)[3]][run == unique(run)[1]][1:3, 1:6]

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.