GSEAparams-class: GSEAparams S4 class implementation in R

In MIGSA: Massive and Integrative Gene Set Analysis

Description

This S4 class contains the parameters to provide for GSEA.

Slots

perm_number

number of permutations for p-value calculation (default: 200).

min_sz

minimum size of gene sets (number of genes in a gene set) to be included in the analysis (default: 5).

pv

estimate of the variance associated with each observation (default: 0).

w1

weight 1, parameter used to calculate the prior variance obtained with class size var.constant. This penalizes especially small classes and small subsets. Values around 0.1 - 0.5 are expected to be reasonable. (default: 0.2).

w2

weight 2, parameter used to calculate the prior variance obtained with the same class size as that of the analyzed class. This penalizes small subsets from the gene list. Values around 0.3 and 0.5 are expected to be reasonable (default: 0.5).

vc

size of the reference class used with wgt1. (default: 10).

See Also

SEAparams-class

summary

Examples

## Lets create the default GSEAparams object.
myGseaParams <- GSEAparams()
## Lets create another GSEAparams object with 500 permutations.
myGseaParams500Perms <- GSEAparams(perm_number = 500)

MIGSA documentation built on Nov. 8, 2020, 8:26 p.m.