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
*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.anamarija at 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 at 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]]
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
?s 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
>
> ______________________________________________
> R-help at 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.
>
On Wed, 18 Dec 2019 12:25:24 -0600 Ana Marija <sokovic.anamarija at gmail.com> wrote:> Error in cor(D[, 18 + exon_offset], D[, 19 + exon_offset]) : > 'x' must be numericTry str(a) to find out the types of the columns. A stray typo could make a representation of a number impossible to parse and make the whole column textual. Use which(is.na(as.numeric(as.character(a[,column_number])))) to find out the row number where it happened (using extra as.character() here in case the column is a factor). -- Best regards, Ivan
Hi Ivan, here it is:> str(a)'data.frame': 17389 obs. of 21 variables: $ V1 : Factor w/ 17389 levels "ENSG00000000419",..: 14093 14622 14705 14651 14784 17138 14773 14163 14569 15156 ... $ V2 : Factor w/ 22 levels "chr1","chr10",..: 1 1 1 1 1 1 1 1 1 1 ... $ V3 : int 29571 36082 91106 133724 173863 200323 259025 297503 348367 493242 ... $ V4 : int 29570 36081 91105 133723 173862 200322 259024 297502 348366 493241 ... $ V5 : Factor w/ 2 levels "-","+": 1 1 1 1 1 1 1 1 1 1 ... $ V6 : int 983 1006 1169 1340 1441 1620 1897 2032 2175 2697 ... $ V7 : int -828479 -38709 -782443 69986 -831895 -980529 -647609 -946918 -631093 -886444 ... $ V8 : Factor w/ 17104 levels "1:10095977:G:GT",..: 7339 4761 2344 7480 12580 4781 14856 3061 9397 6938 ... $ V9 : Factor w/ 22 levels "chr1","chr10",..: 1 1 1 1 1 1 1 1 1 1 ... $ V10 : int 858049 74790 873548 63735 1005757 1180851 906633 1244420 979459 1379685 ... $ V11 : int 858049 74790 873548 63738 1005771 1180851 906633 1244420 979459 1379685 ... $ Effect_allele : Factor w/ 358 levels "A","AAAAACAAAAC",..: 267 190 92 92 54 92 190 1 267 267 ... $ Baseline_allele: Factor w/ 435 levels "A","AAAAAAAAAATAAAAAT",..: 112 112 325 175 1 325 325 237 112 237 ... $ V12 : int 404 404 404 404 404 404 404 404 404 404 ... $ V13 : num 348 347 347 339 342 ... $ V14 : num 1.04 1.03 1.02 1.04 1.04 ... $ V15 : num 140 138 153 154 171 ... $ V16 : num 0.000742 0.002822 0.000626 0.000798 0.002894 ... $ V17 : num 0.269 -0.687 -0.285 -0.398 0.341 ... $ V18 : num 0.196 0.531 0.203 0.265 0.639 ... $ V19 : num 0.198 0.529 0.199 0.261 0.634 ... and this:> which(is.na(as.numeric(as.character(a[,18]))))[1] 10757 11062 11063 11064 11065 11066 11067 11068 11069 11070 11071 11072 [13] 11073 11074 11075> which(is.na(as.numeric(as.character(a[,19]))))[1] 10757 11062 11063 11064 11065 11066 11067 11068 11069 11070 11071 11072 [13] 11073 11074 11075 columns 18 and 19 seems to be numeric, what is could be the issue? On Wed, Dec 18, 2019 at 1:49 PM Ivan Krylov <krylov.r00t at gmail.com> wrote:> > On Wed, 18 Dec 2019 12:25:24 -0600 > Ana Marija <sokovic.anamarija at gmail.com> wrote: > > > Error in cor(D[, 18 + exon_offset], D[, 19 + exon_offset]) : > > 'x' must be numeric > > Try str(a) to find out the types of the columns. A stray typo could > make a representation of a number impossible to parse and make the > whole column textual. Use > which(is.na(as.numeric(as.character(a[,column_number])))) to find out > the row number where it happened (using extra as.character() here in > case the column is a factor). > > -- > Best regards, > Ivan