Hi,
After formating the biom.df and eqtl.df objects and adding a $type column to each, I got two data frames looking this, which seems fine:
head(biom.df)
SNPID CHR POS PVAL BETA SE A1 A2 N type
1 rs141709959 1 751456 0.690541 0.1593330 0.400583 T C 59225 quant
2 rs28527770 1 751756 0.924024 -0.0214828 0.225478 T C 59225 quant
3 rs201062411 1 752308 0.869061 0.0605275 0.367507 I D 59225 quant
4 rs146277091 1 752478 0.869175 0.0604588 0.367412 G A 59225 quant
5 rs3094315 1 752566 0.923839 0.0183066 0.191672 G A 59225 quant
6 rs149886465 1 752617 0.866254 0.0617738 0.367130 C A 59225 quant
head(eqtl.df)
SNPID CHR POS PVAL BETA SE ProbeID A1
1 rs143225517 1 751756 8.375668e-03 0.03676353 0.01388336 ENSG00000228794 T
2 rs143225517 1 751756 7.111666e-03 0.08623658 0.03189537 ENSG00000236239 T
3 rs143225517 1 751756 7.795206e-03 -0.06456827 0.02415937 ENSG00000237491 T
4 rs3094315 1 752566 2.966613e-03 -0.03436617 0.01150450 ENSG00000228794 G
5 rs3094315 1 752566 1.986647e-05 0.08544778 0.01981848 ENSG00000237491 G
6 rs3131972 1 752721 8.914779e-03 -0.02999908 0.01142151 ENSG00000228794 A
A2 F N MAF type
1 C 0.8529771 467 0.1470229 quant
2 C 0.8529771 467 0.1470229 quant
3 C 0.8529771 467 0.1470229 quant
4 A 0.1892925 467 0.1892925 quant
5 A 0.1892925 467 0.1892925 quant
6 G 0.1921606 467 0.1921606 quant
However, when running coloc.eqtl.biom using default parameters, I get this error message, not sure what is causing it:
132 SNPs out of 139 had the correct alleles, discarding SNPs without the correct alleles
There are 0 duplicated SNP names in the data
ENSG00000236239: 132 snps in both biomarker and eQTL data. From: 751756 To: 1874837
Processing dataset
Error in d$type == "quant" :
comparison (1) is possible only for atomic and list types
In addition: Warning message:
In coloc.eqtl.biom(eqtl.df = eqtl.df, biom.df = biom.df, p12 = 1e-06, :
NAs introduced by coercion
Hi,
After formating the biom.df and eqtl.df objects and adding a $type column to each, I got two data frames looking this, which seems fine:
However, when running coloc.eqtl.biom using default parameters, I get this error message, not sure what is causing it:
132 SNPs out of 139 had the correct alleles, discarding SNPs without the correct alleles
There are 0 duplicated SNP names in the data
ENSG00000236239: 132 snps in both biomarker and eQTL data. From: 751756 To: 1874837
Processing dataset
Error in d$type == "quant" :
comparison (1) is possible only for atomic and list types
In addition: Warning message:
In coloc.eqtl.biom(eqtl.df = eqtl.df, biom.df = biom.df, p12 = 1e-06, :
NAs introduced by coercion