Global parameters

Global parameters

cola_opt(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)

Arguments

...

Arguments for the parameters, see "details" section.

RESET

Whether to reset to default values.

READ.ONLY

Please ignore.

LOCAL

Please ignore.

ADD

Please ignore.

Details

There are following global parameters:

group_diff

Used in get_signatures,ConsensusPartition-method to globally control the minimal difference between subgroups.

fdr_cutoff

Used in get_signatures,ConsensusPartition-method to globally control the cutoff of FDR for the differential signature tests.

color_set_2

Colors for the predicted subgroups.

help

Whether to print help messages.

message

Whether to print messages.

Examples

cola_opt
#>  Option      Value                                                                                                                                                  
#>  -----------:-------------------------------------------------------------------
#>  group_diff  0                                                                                                                                                      
#>  fdr_cutoff  0.05                                                                                                                                                   
#>  help        TRUE                                                                                                                                                   
#>  color_set_1 #E41A1C, #377EB8, #4DAF4A, #984EA3, #FF7F00, #FFFF33, #A65628, #F781BF, #999999, #1B9E77, #D95F02, #7570B3, #E7298A, #66A61E, #E6AB02, #A6761D, #666666
#>  color_set_2 #66C2A5, #FC8D62, #8DA0CB, #E78AC3, #A6D854, #FFD92F, #E5C494, #B3B3B3, #7FC97F, #BEAED4, #FDC086, #FFFF99, #386CB0, #F0027F, #BF5B17, #666666         
#>  message     TRUE                                                                                                                                                   
cola_opt$group_diff = 0.2  # e.g. for methylation datasets
cola_opt$fdr_cutoff = 0.1  # e.g. for methylation datasets
cola_opt
#>  Option      Value                                                                                                                                                  
#>  -----------:-------------------------------------------------------------------
#>  group_diff  0.2                                                                                                                                                    
#>  fdr_cutoff  0.1                                                                                                                                                    
#>  help        TRUE                                                                                                                                                   
#>  color_set_1 #E41A1C, #377EB8, #4DAF4A, #984EA3, #FF7F00, #FFFF33, #A65628, #F781BF, #999999, #1B9E77, #D95F02, #7570B3, #E7298A, #66A61E, #E6AB02, #A6761D, #666666
#>  color_set_2 #66C2A5, #FC8D62, #8DA0CB, #E78AC3, #A6D854, #FFD92F, #E5C494, #B3B3B3, #7FC97F, #BEAED4, #FDC086, #FFFF99, #386CB0, #F0027F, #BF5B17, #666666         
#>  message     TRUE                                                                                                                                                   
cola_opt(RESET = TRUE)