readOmics: Read in omics data.

Description

This function reads omics data: differentially expressed genes and relatively differentially abundant proteins with corresponding fold changes for each time point.

Usage

readOmics(tp_prots, tp_genes, omics, PWdatabase, TFtargetdatabase)

Arguments

tp_prots

numeric vector of protein timepoints used in experiment; in case of single time point experiments simply assign an experiment number (e.g. 1).

tp_genes

numeric vector of gene/transcript timepoints used in experiment; in case of single time point experiments simply assign an experiment number (e.g. 1).

omics

list containing protein and gene IDs and fold changes: Input are two lists, one for protein data, one for gene data, both including a vector of all measured IDs as first element and a list as second element including for each tp a dataframe with IDs and foldchanges per timepoint.

PWdatabase

character vector of pathway database names which should be used for pathway identification, possible choices are "biocarta", "kegg", "nci", "reactome".

TFtargetdatabase

character vector of TF target database names which should be used for transcription factor/target gene identification, possible choices are "chea", "pazar", "userspec". In case the user is able to provide an own list of transcription factor target gene matches, he can indicate this via "userspec".

Value

OmicsData object: list of 4 elements (OmicsD, PathwayD, TFtargetsD, Status); OmicsD containing omics data set + results (after analysis); PathwayD containing selected pathway databases + biopax model; TFtargetsD containing selected TF target gene databases + TF target gene data.

Examples

Run this code

data(OmicsExampleData)
data_omics = readOmics(tp_prots = c(0.25, 1, 4, 8, 13, 18, 24),
tp_genes = c(1, 4, 8, 13, 18, 24), OmicsExampleData,
PWdatabase = c("biocarta"),
TFtargetdatabase = c("chea"))

## Not run: 
# data_omics = readOmics(tp_prots = c(0.25, 1, 4, 8, 13, 18, 24),
# tp_genes = c(1, 4, 8, 13, 18, 24), OmicsExampleData,
# PWdatabase = c("biocarta", "kegg", "nci", "reactome"),
# TFtargetdatabase = c("chea", "pazar", "userspec"))
# ## End(Not run)

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