SNPmatch_list: Find SNPs with similar characteristics to the input SNPs.
In ldehoyos/twinSNP: twinSNP package

Description Usage Arguments Details Value Examples

Based on the information provided in the database, the function matches the input SNPs with those SNPs in the database based on the parameters of minor allele frequency, gene density, distance to nearest gene and LD buddies.

1	SNPmatch_list(database, inputSNPs, MAF, GD, DNG, LDB)

`database`	Data frame with information of SNPs
`inputSNPs`	Character vector with the input SNPs in format chr:pos.
`MAF`	Numeric value with interval limits of minor allele frequency.
`GD`	Numeric value with interval limits of gene density.
`DNG`	Numeric value with interval limits of distance to nearest gene.
`LDB`	Numeric value with interval limits of LD buddies.

It also writes the information on the included ("input_snps_annotated.txt") and excluded ("input_snps_excluded.txt") SNPs depending on if they are available on the database.

Also, at the end, if there is any SNP that does not have any match, it will also write it in a txt ("input_snps_annotated_unmatched.txt") and exclude it from the final output ("matched_snps_annotation.txt").

It is different to the function "SNPmatch" as this function outputs a list with the information of the SNPs and its matches, which is also done with the functions "listMatches" and "listMatches2". Thus, this function is better in terms of computation time.

Data table with the input SNPs, their matches and information about the matches.

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myDatabase <- data.frame(snpID= c("10:10001753", "10:10001794"), snp_maf= c(0.074, 0.410), gene_count= c(0,0), dist_nearest_gene_snpsnap= c(98932,98891), friends_ld05= c(35,168))
myVars <- data.frame(input_snp= c("18:53093251", "12:57682956", "10:10001794"))
SNPlist <- SNPmatch_list(database = myDatabase, inputSNPs = myVars, MAF = 0.05, GD = 0.5, DNG = 0.5, LDB = 0.5)