*snip* Error in cor(D[, 18 + exon_offset], D[, 19 + exon_offset]) : 'x' must be numeric *snip*
You are applying the correlation function to non-numeric variables. Brian On Wed, Dec 18, 2019 at 12:23 PM Ana Marija <sokovic.anamar...@gmail.com> wrote: > Hello, > > I was running this code, located at: > https://github.com/swvanderlaan/QTLToolKit/blob/master/SCRIPTS/runFDR_cis.R > > Rscript runFDR_cis.R Retina_new_perms_full.txt 0.05 permutations_all > > and I got this error: > > Processing QTLtools output. > * Input = [ Retina_new_perms_full.txt ] > * FDR = 0.05 > * Output = [ permutations_all ] > > Read Input data. Note: we expect a file with 19 columns i.e. it is > best to use the results from a permutation test. > * Gene level correction detected > * Number of molecular phenotypes = 17375 > * Number of NA lines = 15 > Error in cor(D[, 18 + exon_offset], D[, 19 + exon_offset]) : > 'x' must be numeric > Calls: cat -> cor > Execution halted > > > a=read.table("Retina_new_perms_full.txt", header=T) > > head(a) > V1 V2 V3 V4 V5 V6 V7 > 1 ENSG00000227232 chr1 29571 29570 - 983 -828479 > 2 ENSG00000237613 chr1 36082 36081 - 1006 -38709 > 3 ENSG00000239945 chr1 91106 91105 - 1169 -782443 > 4 ENSG00000238009 chr1 133724 133723 - 1340 69986 > 5 ENSG00000241860 chr1 173863 173862 - 1441 -831895 > 6 ENSG00000279457 chr1 200323 200322 - 1620 -980529 > V8 V9 V10 V11 Effect_allele > 1 rs200956863:793429:T:C chr1 858049 858049 T > 2 rs13328700:74790:C:G chr1 74790 74790 G > 3 rs11240780:808928:C:T chr1 873548 873548 C > 4 rs201888535:63735:CCTA:C chr1 63735 63738 C > 5 rs61703480:941137:AGCCCCCGCAGCAGT:A chr1 1005757 1005771 AGCCCCCGCAGCAGT > 6 rs13374146:1116231:T:C chr1 1180851 1180851 C > Baseline_allele V12 V13 V14 V15 V16 V17 > V18 > 1 C 404 348.489 1.04262 139.753 0.000741814 0.269459 > 0.196180 > 2 C 404 346.832 1.03086 138.165 0.002822220 -0.687290 > 0.530547 > 3 T 404 347.109 1.02189 152.726 0.000626379 -0.284821 > 0.203080 > 4 CCTA 404 338.804 1.04423 154.301 0.000797573 -0.398402 > 0.264974 > 5 A 404 341.822 1.04355 171.178 0.002893770 0.340855 > 0.638936 > 6 T 404 338.232 1.05240 180.879 0.001846080 -0.458547 > 0.528947 > V19 > 1 0.198142 > 2 0.529105 > 3 0.199394 > 4 0.261441 > 5 0.633917 > 6 0.524186 > > > Please advise, > Ana > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
