SNPchiMp

[…] ing GenABEL package [] in R environment, and polymorphisms with a minimum allele frequency (MAF) < 0.05 were discarded for further analysis. In order to be able to compare data from the two platforms SNPchiMp v.3 [] was used to select SNPs overlapping between both. […]

[…] osomes, were obtained by the R package biomaRt (v. 2.30.0) [, ] from the Sus scrofa genome build (10.2, version 79). The chromosomal locations of the SNPs associated with the eQTLs were obtained from SNPchiMp (v. 3) database []. The chromosomal densities of eQTLs were calculated by the number of either unfiltered or filtered eQTLs per chromosome divided by length in bases of the respective chromos […]

[…] Map positions of the SNPs were based on UMD3.1. Information about the markers (rs, map position, alleles) were obtained using the SNPchiMp tool []. When these SNPs were located within a gene, several analyses were carried out. First, the position of the SNP (intronic or exonic, 5´-UTR or 3´-UTR) was determined. Second, repercuss […]

[…] cance thresholds defined by the Bonferroni correction was too conservative. Therefore, the genome-wide suggestive threshold was also defined as; P = 5.0 × 10−5. SNP maps were updated according to the SNPchiMp v.2 database [] and the Sscrofa 10.2 assembly. The positional candidate genes within the range of 1 Mb bin size of the significant region were scanned using the NCBI2R R-package []. r2 values […]

[…] The SNPchiMp database [] was used to convert the Illumina SNP name to the rsID (the SNP accession number used to search a SNP in all public databases). The rsID was used in NCBI database (http://www.ncbi. […]