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seed2partners_ftest

seed2partners_ftest.Rd

This function will perform fisher exact test with seed and partner driver regulons. SINBA_originalID,target_list,N,padjust_method=

Usage

seed2partners_ftest(
  SINBA_originalID = NULL,
  target_list = NULL,
  N,
  padjust_method = "BH"
)

Arguments

SINBA_originalID

character vector, the seed-partner driver pairs, seed gene name and partner gene name are seperated by colon. SINBA_originalID can be manually created or generated by combineNet2target_list with return_type="SINBA_originalID".

target_list

list, the driver-to-target list object. target_list is generated by get.combined.network and contains all the driver gene regulons.

N

numeric, total unique genes in the whole network or the target_list.

padjust_method

character,the type of p value correction methods. User can choose from c ("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"). Default is "BH".

Value

return a table of fisher exact test.

Examples

sinba_target_list<-combineNet2target_list(target_list=SINBA.par$combined.network$target_list,seed_name="LCK",partner_name=c("BCL2","FYN"),return_type="SINBA_target_list")
#> Error in combineNet2target_list(target_list = SINBA.par$combined.network$target_list,     seed_name = "LCK", partner_name = c("BCL2", "FYN"), return_type = "SINBA_target_list"): could not find function "combineNet2target_list"
sinba_originalID<-combineNet2target_list(target_list=SINBA.par$combined.network$target_list,seed_name="LCK",partner_name=c("BCL2","FYN"),return_type="SINBA_originalID")
#> Error in combineNet2target_list(target_list = SINBA.par$combined.network$target_list,     seed_name = "LCK", partner_name = c("BCL2", "FYN"), return_type = "SINBA_originalID"): could not find function "combineNet2target_list"
sinba_originalID<-as.character(sinba_originalID$originalID)
#> Error: object 'sinba_originalID' not found
N<-length(unique(c(SINBA.par$combined.network$network_dat$source,SINBA.par$combined.network$network_dat$target)))
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'unique': object 'SINBA.par' not found

f_df<-seed2partners_ftest(SINBA_originalID=sinba_originalID,target_list=SINBA.par$combined.network$target_list,N=N)
#> Error in seed2partners_ftest(SINBA_originalID = sinba_originalID, target_list = SINBA.par$combined.network$target_list,     N = N): could not find function "seed2partners_ftest"
if (FALSE) { # \dontrun{
} # }