Tissue Specific Markers

[andrewdchen]

Hello! Think this is a great tool, but was wondering how tissue specific markers were compiled? And how we would try extending existing databases i.e. if I want to add several breast specific markers to be run alongside the other breast markers already in the database, is there a recommended way to do this?

[chloelulu]

Hi @andrewdchen, thanks for your interest in our tool and sorry for the late reply. Below code use the demodata(data(demodata)) as an example of your markers.

scMayoMapDatabase2 <- reshape2::melt(scMayoMapDatabase,id.vars= c('tissue','gene'))
yourDB <- demodata %>% mutate(variable = paste0('breast: ',celltype)) %>% dplyr::select(-celltype) %>% # add the column of tissue type with cell types
  mutate(tissue = 'breast',gene = toupper(gene)) # add tissue name, convert gene into uppercase
newDB <- rbind(scMayoMapDatabase2, yourDB) # combine the scMayoDatabase with your marker pool, please make sure they are in the same format. 
newDB <- unique(newDB) # exclude the duplicates, sometimes the markers you supplied already exist in the scMayoDatabase
db <- tidyr::spread(newDB, key = c('variable'), value = 'value')
db[is.na(db)] <- 0
obj <- scMayoMap(data = data, tissue = 'breast', database = db)

Don't hesitate to reach out if you meet any issue in the application!