get_results {genomicper}

Circular Permutation Results

Description

Creates a summary dataframe of the genomic permutations datasets

Usage

get_results(res_pattern="Permus",level="snp",from="workspace",
threshold=0.05,envir = "")

Arguments

res_pattern

Pattern of the Permutation files/variable. eg. res=pattern="Permus"

level

Permutation level performed.level values "snp" or "gene"

from

Location of the permutation datasets.from values "workspace" or "directory"

threshold

Threshold of significance set

envir

R environment where save the data to

Value

results

Data frame with Pathway ID, Trait, Threshold set by permutations,
Gene results include the theoretical hypergeometric p-value and the,
observed (Empirical Hypergeometric p-values)
SNP results include the count of significan SNPs and the overall score
Score is the proportion of tests observed with more significant results

Format

## SNP level results
     PathID    Trait Threshold RealCount Score
1  hsa00010     abpi         0         0 0.037
2  hsa00010 abpildfa         0         0 0.040
3  hsa04720     abpi         2         0 0.311	
## Gene level results	
     PathID Trait   Threshold     P-Value  Observed
1  hsa00010  abpi 0.040441176 0.058823529 1.0000000
2  hsa00020  abpi 0.000000000 0.000000000 0.1666667
3  hsa00030  abpi 0.040441176 0.058823529 1.0000000

Examples

data(demo,SNPsAnnotation)
all_data <- read_pvals(data_name=demo,snps_ann=SNPsAnnotation)
genome_results <-genome_order(all_data=all_data)
	# Results from genome_order
	ordered_alldata <- genome_results$ordered_alldata
	gs_locs <- genome_results$gs_locs

# Create new environment to save data
gper.env <- new.env()

# Get pathways
data(RHSA164843,RHSA446343,RHSA8876384,RHSA8964572,RHSA109582,RHSA1474244,envir=gper.env)

paths_res <- read2_paths(ordered_alldata=ordered_alldata,gs_locs=gs_locs,
sets_from="workspace",sets_prefix="RHSA",level="snp",envir=gper.env)
		pers_ids <- paths_res$per_ors
		pathways<- paths_res$pathways

snps_permutation(ordered_alldata=ordered_alldata,pers_ids=pers_ids,
ntraits=c(7,9),nper=10,saveto="workspace",threshold=0.05,
gs_locs=gs_locs,envir= gper.env)

results <- get_results(res_pattern="Permus",level="snp",
from="workspace",threshold=0.05,envir = gper.env)