TCGAbiolinks (version 1.2.5)

TCGAquery_Investigate: Find most studied TF in pubmed related to a specific cancer, disease, or tissue

Description

Find most studied TF in pubmed related to a specific cancer, disease, or tissue

Usage

TCGAquery_Investigate(tumor, dataDEGsFiltLevelTF, topgenes)

Arguments

tumor

is character such as cancer, disease, or tissue eg. BRCA or breast

dataDEGsFiltLevelTF

is a table output from TCGAanalyze_LevelTab with only TFs

topgenes

is the number of top genes (eg. 10) in the rownames(dataDEGsFiltLevelTF) where find in pubmed if those genes or TFs are already related to that cancer or disease

Value

table with number of pubmed's publications related to tfs and disease selected

Examples

query <- TCGAquery(tumor = "lgg")
## Not run: 
# TFs <- EAGenes[EAGenes$Family =="transcription regulator",]
# TFs_inDEGs <- intersect(TFs$Gene, dataDEGsFiltLevel$mRNA )
# dataDEGsFiltLevelTFs <- dataDEGsFiltLevel[TFs_inDEGs,]
# dataDEGsFiltLevelTFs <- dataDEGsFiltLevelTFs[order(dataDEGsFiltLevelTFs$Delta,decreasing = TRUE),]
# # Find Pubmed of TF studied related to cancer
# tabDEGsTFPubmed <- TCGAquery_Investigate("breast", dataDEGsFiltLevelTFs, topgenes = 1)
# ## End(Not run)