read_pvals: Read GWAS p-values of association and Merge with SNP annotations

Description

Read GWAS p-values of association and Merge with SNP annotations for analysis

Usage

read_pvals(data_name="",snps_ann="",from="workspace")

Arguments

data_name

GWAS p_values (tab delimited file)(SNP_IDs Trait1 Trait2 ...TraitN)

snps_ann

SNPs Annotation (SNPsAnnotation). Genomicper uses entrez gene ids to annotate associate SNPs-to genes-pathways The annotation MUST match your data input (coordinates and chromosome format) Any SNP ID is valid, as long the ID is set as character The examples below show an option on how to annotate the SNPs prior the use of genomicper

from

Datasets location. Values "workspace" OR "directory"

Value

Dataframe: name; chromosome; Location; GeneID; Symbol; Orientation; Trait1; TraitN

Formats

GWAS p_values (tab delimited file)(SNP_IDs Trait1 Trait2 ...TraitN) name Trait1 Trait2 TraitN rs10000010 0.9122360 0.30088096 0.2332038 rs10000023 0.8642906 0.52064064 0.9243443 rs10000030 0.2832705 0.99021664 0.8359339

SNPs Annotation (SNPsAnnotation) name Chromosome Location GENE_ID Symbol Orientation rs1000313 1 15405489 23254 KIAA1026 + rs1000533 1 168282491 9095 TBX19 + rs1000731 1 231963491 27185 DISC1 +

Output: name Chromosome Location GENE_ID Symbol Orientation Trait1 rs10000010 4 21618674 80333 KCNIP4 - 0.9122360 rs10000023 4 95733906 658 BMPR1B + 0.8642906 rs10000030 4 103374154 NA <NA> <NA> 0.2832705

Examples

Run this code

# NOT RUN {
## DEMO // WORKSPACE
data(demo,SNPsAnnotation)
all_data <- read_pvals(data_name=demo,snps_ann=SNPsAnnotation)
# }