generate_new_snp_ids: Get new snp ids for snps not found in ref db.

In nehiljain/genewiseR: A tool to perform pool gwas analysis in R,

Description

The function takes in the data frame after attaching snp ids from the ref. using get_snp_ids(). The function computes the length of missing snp_name. It assumes

Usage

generate_new_snp_ids(study_df, prefix_str = "dal_snp")

Arguments

prefix_str	a chacracter value used as prefix to numerical index of the snps, default is 'dal_snp'
study_dfthe	study dataframe/data.table

Value

a datatable with all missing snp ids changed to dal_snp1, dal_snp2,.... The column with the ids is snp_id

Examples

# combine_gwas_df <- dir_rbind("../genewiseR_data/raw_data/",
#header = F,col_names = c("chr","pos","allele","p_value"))

#ref_df <- read_tsv("../genewiseR_data/ref/indels.Bos_taurus.vcf", 
#comment = "##", progress = T, trim_ws = T, col_types = "cicccnnc")

#result_df <- get_snp_ids(combine_gwas_df, ref_df, out_file_path = "../genewiseR_data/tmp.tsv" )

#with_ids_dt <- generate_new_snp_ids(result_df)

nehiljain/genewiseR documentation built on May 23, 2019, 1:31 p.m.