get_snpset {topr} | R Documentation |
Create a dataframe that can be used as input for making effect plots
Description
get_snpset()
Usage
get_snpset(
df1,
df2,
thresh = 5e-08,
protein_coding_only = TRUE,
region_size = 1e+06,
verbose = NULL,
show_full_output = FALSE,
build = 38,
format = "wide"
)
Arguments
df1 |
The dataframe to extract the top snps from (with p-value below thresh) |
df2 |
The dataframe in which to search for overlapping SNPs from dataframe1 |
thresh |
A number. P-value threshold, only extract variants with p-values below this threshold (5e-08 by default) |
protein_coding_only |
Logical, set this variable to TRUE to only use protein_coding genes for annotation |
region_size |
An integer (default = 20000000) (or a string represented as 200kb or 2MB) indicating the window size for variant labeling. Increase this number for sparser annotation and decrease for denser annotation. |
verbose |
Logical, (default: FALSE). Assign to TRUE to get information on which alleles are matched and which are not. |
show_full_output |
A logical scalar (default:FALSE). Assign to TRUE to show the full output from this function |
build |
A string, genome build, choose between builds 37 (GRCh37) and 38 (GRCh38) (default is 38) |
format |
A string, representing either wide or long format (default : "wide"). By default a snpset created from two dataframes is returned in a wide format. |
Value
Dataframe of overlapping snps (snpset)
Examples
## Not run:
CD_UKBB_index_snps <-get_lead_snps(CD_UKBB)
get_snpset(CD_UKBB_index_snps, CD_FINNGEN)
## End(Not run)