Prepare summary table with statistically significant associations
Source:R/helpers-rmd.R
prep_assoc_summary.RdPrepare summary table with statistically significant associations
Usage
prep_assoc_summary(
dir_path,
ls_file,
alpha = 0.05,
n_stat_sig_row = 10,
read_file_fun = readxl::read_excel,
as_list = FALSE
)Arguments
- dir_path
A string path to the directory containing files with associations data.
- ls_file
A character vector with names of files containing associations data.
- alpha
A numeric cutoff to identify statistically significant correlations
- n_stat_sig_row
A numeric value specifying the maximum number of statistically significant associations (rows) to include from each file.
- read_file_fun
A function to read the data from file; default is
readxl::read_excel- as_list
A logical flag indicating whether the result should be returned as a list or as a table.
Value
A DT::datatable object.
Author
Janina Smoła janina.smola@external.roche.com
Examples
dir_path <- system.file("testdata", package = "gDRplots")
ls_file <- list.files(dir_path, pattern = "[.]xlsx$")
prep_assoc_summary(dir_path = dir_path, ls_file = ls_file)
#> feature response rho q_value neglog_q_value
#> <char> <char> <num> <num> <num>
#> 1: NU_023_X1W GR_gDR_log10_xc50 -0.15 0.0070 2.154902
#> 2: NU_017_X1Q GR_gDR_log10_xc50 -0.50 0.0295 1.530178
#> 3: NU_011_X1K GR_gDR_log10_xc50 1.25 0.0355 1.449772
#> 4: GRP_007_XC GR_gDR_log10_xc50 0.75 0.0190 1.721246
#> 5: GRP_006_XC GR_gDR_x_max 0.05 0.0035 2.455932
#> 6: GRP_021_XC GR_gDR_x_max 0.05 0.0035 2.455932
#> 7: GRP_002_XC GR_gDR_x_max 0.40 0.0060 2.221849
#> 8: GRP_025_XC GR_gDR_x_max 0.05 0.0110 1.958607
#> 9: GRP_009_XC GR_gDR_x_max -1.00 0.0135 1.869666
#> 10: GRP_020_XC GR_gDR_x_max -0.30 0.0235 1.628932
#> 11: GRP_010_XC GR_gDR_x_max 0.05 0.0285 1.545155
#> 12: GRP_008_XC GR_gDR_x_max -0.65 0.0310 1.508638
#> 13: GRP_001_XC GR_gDR_x_max -1.00 0.0335 1.474955
#> 14: GRP_017_XC GR_gDR_x_max -0.30 0.0460 1.337242
#> 15: NU_006_X1F RV_gDR_x_max 0.05 0.0035 2.455932
#> 16: NU_021_X1U RV_gDR_x_max 0.05 0.0035 2.455932
#> 17: NU_002_X1B RV_gDR_x_max 0.40 0.0060 2.221849
#> 18: NU_025_X1Y RV_gDR_x_max 0.05 0.0110 1.958607
#> 19: NU_009_X1I RV_gDR_x_max -1.00 0.0135 1.869666
#> 20: NU_020_X1T RV_gDR_x_max -0.30 0.0235 1.628932
#> 21: NU_010_X1J RV_gDR_x_max 0.05 0.0285 1.545155
#> 22: NU_008_X1H RV_gDR_x_max -0.65 0.0310 1.508638
#> 23: NU_001_X1A RV_gDR_x_max -1.00 0.0335 1.474955
#> 24: NU_017_X1Q RV_gDR_x_max -0.30 0.0460 1.337242
#> 25: NU_023_X1W RV_gDR_x_mean -0.15 0.0070 2.154902
#> 26: NU_017_X1Q RV_gDR_x_mean -0.50 0.0295 1.530178
#> 27: NU_011_X1K RV_gDR_x_mean 1.25 0.0355 1.449772
#> 28: GRP_016_XC RV_gDR_x_mean 0.55 0.0485 1.314258
#> feature response rho q_value neglog_q_value
#> <char> <char> <num> <num> <num>
#> src
#> <char>
#> 1: tab_assoc_GR__featNUX_drug_003_GR_gDR_log10_xc50.xlsx
#> 2: tab_assoc_GR__featNUX_drug_003_GR_gDR_log10_xc50.xlsx
#> 3: tab_assoc_GR__featNUX_drug_003_GR_gDR_log10_xc50.xlsx
#> 4: tab_assoc_GR__metaGRP_drug_001_GR_gDR_log10_xc50.xlsx
#> 5: tab_assoc_GR__metaGRP_drug_001_GR_gDR_x_max.xlsx
#> 6: tab_assoc_GR__metaGRP_drug_001_GR_gDR_x_max.xlsx
#> 7: tab_assoc_GR__metaGRP_drug_001_GR_gDR_x_max.xlsx
#> 8: tab_assoc_GR__metaGRP_drug_001_GR_gDR_x_max.xlsx
#> 9: tab_assoc_GR__metaGRP_drug_001_GR_gDR_x_max.xlsx
#> 10: tab_assoc_GR__metaGRP_drug_001_GR_gDR_x_max.xlsx
#> 11: tab_assoc_GR__metaGRP_drug_001_GR_gDR_x_max.xlsx
#> 12: tab_assoc_GR__metaGRP_drug_001_GR_gDR_x_max.xlsx
#> 13: tab_assoc_GR__metaGRP_drug_001_GR_gDR_x_max.xlsx
#> 14: tab_assoc_GR__metaGRP_drug_001_GR_gDR_x_max.xlsx
#> 15: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_max.xlsx
#> 16: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_max.xlsx
#> 17: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_max.xlsx
#> 18: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_max.xlsx
#> 19: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_max.xlsx
#> 20: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_max.xlsx
#> 21: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_max.xlsx
#> 22: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_max.xlsx
#> 23: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_max.xlsx
#> 24: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_max.xlsx
#> 25: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_mean.xlsx
#> 26: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_mean.xlsx
#> 27: tab_assoc_RV__featNUX_drug_001_RV_gDR_x_mean.xlsx
#> 28: tab_assoc_RV__metaGRP_drug_002_RV_gDR_x_mean.xlsx
#> src
#> <char>