getIntersection: Get the SNP set common to/intersection of the ASE calling and...

In karishdsa/ERASE: Extended Randomization for Assessment of Multiple Annotation Enrichment in ASE Datasets

Description

Get the SNP set common to/intersection of the ASE calling and SNP annotation datasets

Usage

getIntersection(df_ase, df_snpAnn, snpAnnType = "GWAS",
  snpAnnCol2Sel = "p")

Arguments

df_ase	- a data frame object containing the SNPs from the ASE calling dataset with a column named 'cmp.col' e.g. containing the rsid, chr:pos values to be compared with the SNP Annotation data It should also have the following columns: 1. with values to be accounted for during randomization e.g. the average read depth and 2. with values to assess the ASE significance e.g. FDR, p-value
df_snpAnn	- data frame object with the SNP annotation data. It must have the column name 'cmp.col' - see df_ase above and a column to rank the SNPs by during randomization
snpAnnType	- is the code for the SNP annotation default is GWAS if the snpAnnType is GWAS, then first, the pvals with value 0 are updated to next.min*1e-100 ; SNPs with > 1 pval are assigned the min pval
snpAnnCol2Sel	- the column name in the SNP annotaion data to be used to rank the SNPs during randomization- e.g. 'p' for GWAS default is 'p' i.e. p-value for GWAS , the default snpAnnType

Value

a dataframe object with SNPs common to the ASE calling and SNP annotation dataset with the snpAnnCol2Sel added to the columns present in df_ASE

karishdsa/ERASE documentation built on May 9, 2019, 2:55 p.m.