print.traseR: Print the outcome of taSNP enrichment analyses

In traseR: GWAS trait-associated SNP enrichment analyses in genomic intervals

Description

Print the outcome of taSNP enrichment analyses. Print the overall taSNP enrichment, trait-specific taSNP enrichment,trait-class-specific taSNP enrichment.

Usage

	## S3 method for class 'traseR'
print(x,isTopK1=FALSE,topK1=10,isTopK2=FALSE,topK2=10,trait.threshold=10,traitclass.threshold=10,...)

Arguments

x	Object returned from traseR
isTopK1	If isTopK1 is TRUE, topK1 traits are printed; otherwise, traits with p-value below Bonferroni correction threshold are printed. Default is FALSE.
topK1	Top K1 traits are printed. Default is 10.
isTopK2	If isTopK2 is TRUE, topK2 trait class are printed; otherwise, trait class with p-value below Bonferroni correction threshold are printed. Default is FALSE.
topK2	Top K2 trait class are printed. Default is 10.
trait.threshold	Traits above this threshold are reported. Default is 10.
traitclass.threshold	Trait class above this threshold are reported. Default is 10.
...	Other parameters to print

Value

Print a data frame of traits ranked by p-value

Author(s)

Li Chen <[e-mail]>, Zhaohui S.Qin<[e-mail]>

Examples

	data(taSNP)
	data(Tcell)
	x=traseR(snpdb=taSNP,region=Tcell)
	print(x)

traseR documentation built on Nov. 8, 2020, 6:55 p.m.