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

Description Usage Arguments Value Examples

View source: R/pwOmics_read_data.R

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

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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

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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")) 
## Not run: 
data_omics = readTFdata(data_omics, 
TF_target_path = system.file("extdata", "TF_targets.txt", 
package = "pwOmics"))

## End(Not run)

pwOmics documentation built on May 20, 2017, 9:25 p.m.

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