TMT {DEP} | R Documentation

## TMT workflow

### Description

`TMT` is a wrapper function running the entire differential enrichment/expression analysis workflow for TMT-based proteomics data. The protein table from IsobarQuant is used as direct input.

### Usage

    TMT(proteins, expdesign, fun = c("man", "bpca", "knn", "QRILC", "MLE",
      "MinDet", "MinProb", "min", "zero", "mixed", "nbavg"), type = c("all",
      "control", "manual"), control = NULL, test = NULL,
      name = "gene_name", ids = "protein_id", alpha = 0.05, lfc = 1)

### Arguments

`proteins` | Data.frame, The data object.
`expdesign` | Data.frame, The experimental design object.
`fun` | "man", "bpca", "knn", "QRILC", "MLE", "MinDet", "MinProb", "min", "zero", "mixed" or "nbavg", Function used for data imputation based on `manual_impute` and `impute`.
`type` | 'all', 'control' or 'manual', The type of contrasts that will be generated.
`control` | Character(1), The sample name to which the contrasts are generated (the control sample would be most appropriate).
`test` | Character, The contrasts that will be tested if type = "manual". These should be formatted as "SampleA_vs_SampleB" or c("SampleA_vs_SampleC", "SampleB_vs_SampleC").
`name` | Character(1), Name of the column representing gene names.
`ids` | 'Character(1), Name of the column representing protein IDs.
`alpha` | Numeric(1), sets the false discovery rate threshold.
`lfc` | Numeric(1), sets the log fold change threshold.

### Value

A list of 8 objects:

`se` | SummarizedExperiment object containing the original data
`filt` | SummarizedExperiment object containing the filtered data
`norm` | SummarizedExperiment object containing the normalized data
`imputed` | SummarizedExperiment object containing the imputed data
`diff` | SummarizedExperiment object containing FDR estimates of differential expression
`dep` | SummarizedExperiment object annotated with logical columns indicating significant proteins
`results` | data.frame containing containing all results variables from the performed analysis
`param` | data.frame containing the test parameters

### Examples

    ## Not run:

    TMT_res <- TMT()

    ## End(Not run)

[Package DEP version 1.12.0 Index]