Hello,
It's hard to tell without data but:
1) The data is read in in code line 19. Check if it has 19 columns and
if columns 18 and 19 are numeric.
If they are of class factor run
D[18:19] <- lapply(D[18:19], function(x) as.numeric(as.character(x)))
2) code line nr 20 is
exon_offset = ifelse(ncol(D) == 19, 0, 2)
So if the data has 19 columns, as expected, exon_offset = 0.
3) The error comes from computing the correlation between D[, 18 +
exon_offset] and D[, 19 + exon_offset] in code line 27:
cat(" * Correlation between Beta approx. and Empirical p-values =",
round(cor(D[, 18+exon_offset], D[, 19+exon_offset]), 4), "\n")
This includes cor(D[, 18+exon_offset], D[, 19+exon_offset])
So check what are the values of ncol(D) and of exon_offset. Their sum
cannot be bigger than ncol(D).
If none of the above, say something.
Hope this helps,
Rui Barradas
Às 18:25 de 18/12/19, Ana Marija escreveu:
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
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