overlap_annot_list: Find the overlapping SNPs between a list of dataframes...

In RHReynolds/LDSCforRyten: Run LDSC on Ryten Lab Server

Description

Function that can, in principle, be used to overlap any list of dataframes containing CHR, BP with a single genomic ranges object. In practice, this function is used to find the overlap between a list of dataframes containing genomic regions within an annotation (e.g. could be genomic coorgindates for SNPs or genes found within the annotation) and the baseline model. Any regions that are found to overlap will be assigned a value of 1 in the newly created 'Binary' column.

Usage

overlap_annot_list(list, query_GR, seqname_col, start_col, end_col, cores = 2)

Arguments

list	List with dataframes containing genomic regions to be overlapped with the query_GR.
query_GR	Genomic ranges object which user wants to query – this will typically be the SNPs in the baseline model.
seqname_col	Column name for column in inputted dataframes referencing chromosome.
start_col	Column name for column in inputted dataframes referencing start BP for search.
end_col	Column name for column in inputted dataframes referencing end BP.
cores	integer. Number of cores to parallelise across. Default = 2.

Value

List of dataframes with SNPs overlapping between input dataframes and query genomic ranges object.

RHReynolds/LDSCforRyten documentation built on Sept. 27, 2021, 5:20 p.m.