bootstrapNull: Bootstrap null distribution of F statistics for FDR...

Description Usage Arguments Value Examples

View source: R/null_bootstrap_funcs.R

Description

Bootstrap null distribution of F statistics for FDR estimation

Usage

1
2
3
4
5
bootstrapNull(df, maxit = 500, independentFiltering = FALSE,
  fcThres = 1.5, minObs = 20, optim_fun_h0 = .min_RSS_h0,
  optim_fun_h1 = .min_RSS_h1_slope_pEC50, optim_fun_h1_2 = NULL,
  gr_fun_h0 = NULL, gr_fun_h1 = NULL, gr_fun_h1_2 = NULL,
  ncores = 1, B = 20, byMsExp = TRUE)

Arguments

df

tidy data_frame retrieved after import of a 2D-TPP dataset, potential filtering and addition of a column "nObs" containing the number of observations per protein

maxit

maximal number of iterations the optimization should be given, default is set to 500

independentFiltering

boolean flag indicating whether independent filtering should be performed based on minimal fold changes per protein profile

fcThres

numeric value of minimal fold change (or inverse fold change) a protein has to show to be kept upon independent filtering

minObs

numeric value of minimal number of observations that should be required per protein

optim_fun_h0

optimization function that should be used for fitting the H0 model

optim_fun_h1

optimization function that should be used for fitting the H1 model

optim_fun_h1_2

optional additional optimization function that will be run with paramters retrieved from optim_fun_h1 and should be used for fitting the H1 model with the trimmed sum model, default is NULL

gr_fun_h0

optional gradient function for optim_fun_h0, default is NULL

gr_fun_h1

optional gradient function for optim_fun_h1, default is NULL

gr_fun_h1_2

optional gradient function for optim_fun_h1_2, default is NULL

ncores

numeric value of numbers of cores that the function should use to parallelize

B

numeric value of rounds of bootstrap, default: 20

byMsExp

boolean flag indicating whether resampling of residuals should be performed separately for data generated by different MS experiments, default TRUE, recommended

Value

data frame containing F statistics of proteins with permuted 2D thermal profiles that are informative on the Null distribution of F statistics

Examples

1
2
3
4
5
6
7
data("simulated_cell_extract_df")
temp_df <- simulated_cell_extract_df %>% 
  filter(clustername %in% paste0("protein", 1:3)) %>% 
  group_by(representative) %>% 
  mutate(nObs = n()) %>% 
  ungroup 
boot_df <- bootstrapNull(temp_df, B = 2/10)  

nkurzaw/TPP2D documentation built on Aug. 17, 2019, 11:26 a.m.