pseudocount: pseudocount of cobindR configuration object

In cobindR: Finding Co-occuring motifs of transcription factor binding sites

Description

pseudocount of cobindR configuration object. Set to 10 as default

Usage

## S4 method for signature 'configuration'
pseudocount(x)
## S4 replacement method for signature 'configuration,character'
pseudocount(x) <- value

Arguments

x	a cobindR configuration object
value	pseudocount for detrending analysis, i.e. the default number in each distance bin.

Value

pseudocount (numeric)

Author(s)

Rob Lehmann <[e-mail]>

See Also

id,experiment_description,sequence_source,sequence_origin,sequence_type,bg_sequence_source,bg_sequence_origin,bg_sequence_type,species,downstream,upstream,max_distance,pairs,pfm_path,threshold,fdrThreshold,path,mart,pseudocount,pValue

Examples

cfg <- cobindRConfiguration()
pseudocount(cfg)

Example output

Warning: namespace 'rtracklayer' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: namespace 'rtracklayer' is not available and has been replaced
by .GlobalEnv when processing object ''

Attaching package: 'cobindR'

The following object is masked from 'package:base':

    sequence

Warning messages:
1: multiple methods tables found for 'organism' 
2: multiple methods tables found for 'species' 
3: multiple methods tables found for 'seqinfo' 
4: multiple methods tables found for 'seqinfo<-' 
5: multiple methods tables found for 'seqnames' 
6: replacing previous import 'BiocGenerics::organism' by 'BSgenome::organism' when loading 'cobindR' 
7: replacing previous import 'BiocGenerics::species' by 'BSgenome::species' when loading 'cobindR' 
8: multiple methods tables found for 'species' 
9: multiple methods tables found for 'path' 
10: multiple methods tables found for 'path<-' 
Warning message:
In .local(.Object, ...) :
  no config-file defined, generating configuration-object with default values
[1] 1

cobindR documentation built on April 28, 2020, 6:40 p.m.