readTFdata: Reads in chosen transcription factor target database...

In pwOmics: Pathway-based data integration of omics data

Description

This function reads in transcription factor information given the selected transcription factor target gene database. The information is downloaded via the AnnotationHub package and merged, if necessary.

Usage

readTFdata(data_omics, TF_target_path, cell_match = 0,
  TF_filter_threshold = 0)

Arguments

data_omics	OmicsData object.
TF_target_path	character vector indicating path of the txt file of matching transcription factors and target genes; the file should be a txt file with first column transcription factors and second column target gene symbols without a header.
cell_match	character indicating the cell line/cells for which the TF target gene data should be extracted from the database; this is only possible for chea database. Available cell-specific data from chea for matching are "Hs578T", "Raji B cells and iDC", "MCF7", "THP-1", "Hela cells", "STHdh", "H3396 breast cancer cells","HL60","HESC","T-ALL", "HPC-7", "ovarian surface epithelium", "HaCaT", "HCT116","U2OS", "Wilms tumor-derived CCG99-9611", "HepG2","HUMAN INTESTINAL CELL LINE CACO-2", "HEK293T","K562", "AK7", "NEUROBLASTOMA","JURKAT","T-47D","LS174T", "MULTIPLE HUMAN CANCER CELL TYPES", "501MEL", "PC3", "CACO-2", "FETAL_BRAIN", "HELA", "U937_AND_SAOS2", "CD4_POS_T", "ERYTHROLEUKEMIA", "RHABDOMYOSARCOMA", "293T", "SW620", "LYMPHOBLASTOID", "VCAP", "SK-N-MC", "CADO-ES1", "MEDULLOBLASTOMA", "M12", "K562_HELA_HEPG2_GM12878", "NT2", "SHEP-21N", "LN229_GBM", "MCF-7", "MELANOMA", "MYOFIBROBLAST", "NTERA2", "MEGAKARYOCYTES", "HMVEC", "ZR75-1", "TREG", "TLL", "A2780", "MONOCYTES", "BEAS2B", "LNCAP PROSTATE CANCER CELL LINES", "MCF10A", "GC-B", "BL", "IMR90", "EOC", "PCA", "PROSTATE_CANCER", "OVCAR3", "MALME-3M", "HFKS", "HEK293", "HELA-AND-SCP4", "CD34+", "IB4-LCL", "MDA-MB-231", "U87", "T47D", "Z138-A519-JVM2", "DLD1", "ATHEROSCLEROTIC-FOAM", "LCL-AND-THP1", "NB4", "PFSK-1 AND SK-N-MC", "EP156T","GBM1-GSC","CD4+", "FIBROSARCOMA", "LGR5+ INTESTINAL STEM CELL","NEUROBLASTOMA BE2-C". If no tissue is given the data from all cells/cell lines are merged.
TF_filter_threshold	integer defining a threshold number to filter out those transcription factors having higher numbers of target genes than 'TF_filter_threshold' from the further analysis

Value

OmicsData object - a list containing information about the user data (timepoints, IDs, fold changes) and the selected databases chosen for the analysis.

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

## Not run: 
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", "kegg", "nci", "reactome"), 
TFtargetdatabase = c("userspec"))
data_omics = readPhosphodata(data_omics, 
phosphoreg = system.file("extdata", "phospho_reg_table.txt", 
package = "pwOmics.newupdown")) 
data_omics = readTFdata(data_omics, 
TF_target_path = system.file("extdata", "TF_targets.txt", 
package = "pwOmics.newupdown"))

## End(Not run)

pwOmics documentation built on Nov. 8, 2020, 4:55 p.m.