setParameters {NoRCE} | R Documentation

## Set the parameters

### Description

Parameters: upstream: Upstream distance from the transcription start position downstream: Downstream distance from the transcription end position searchRegion: Search space of the cis-region. Possible values are "all", "exon", "intron" GOtype: Hierarchical category of the GO ontology. Possible values are "BP", "CC", "MF" pCut: Threshold value for the pvalue. Default value is 0.05 pAdjCut: Cutoff value for the adjusted p-values using one of given method. Default value is 0.05. pAdjust: Methods of the adjusted p-values. Possible methods are "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none" min: Minimum number of genes that are required for enrichment. By default, this value is set to 5. cellline: Cell lines for TAD regions. corrMethod Correlation coeffient method that will be used for evaluation. Possible values are "pearson", "kendall", "spearman" varCutoff: Variance cutt off that genes have less variance than this value will be trimmed pcut: P-value cut off for the correlation values alternate: Holds the alternative hypothesis and "two.sided", "greater" or "less" are the possible values. conf: Confidence level for the returned confidence interval. It is only used for the Pearson correlation coefficient if there are at least 4 complete pairs of observations. minAbsCor: Cut-off value for the Pearson correlation coefficient of the miRNA-mRNA pathwayType: Pathway database for enrichment. Possible values are 'reactome' for Reactome, 'kegg' for KEGG, 'wiki' for WikiPathways, 'other' for custom database enrichTest: Types of enrichment methods to perform enrichment analysis. Possible values are "hyper"(default), "binom", "fisher", "chi". isSymbol: Boolean variable that hold the gene format of the gmt file. If it is set as TRUE, gene format of the gmt file should be symbol. Otherwise, gene format should be ENTREZ ID. By default, it is FALSE.

### Usage

    setParameters(type, value)

### Arguments

`type` | List of parameter names
`value` | New values for the parameters. Value and the parameter names must be in the same order.

### Value

changed parameters

### Examples

    type <- c('downstream','upstream')

    value <- c(2000,30000)

    setParameters(type,value)

[Package NoRCE version 1.4.0 Index]