Help: errors while trying to use my own data

[alishaaman]

I have been trying to draw the plots but with eQTL variant P values from GTEx instead. I have the 1000G data converted to HapMap format and the association data contains the same columns as the example file provided, just the p-value is of an eQTL instead of a GWAS p-value. The annotation file was downloaded from Gencode.

I am just stuck due to multiple errors, the latest one being:

IntGenicPlot('ENST00000515776',gtf=gtf_hmgcr,association=association_hmgcr,hapmap=hapmap_hmgcr, hapmap_ld = NULL,threshold=NULL,up=100000,down=100000,leadsnpLD = FALSE, marker2highlight=NULL,link2gene=NULL,link2LD=marker2link, marker2label=NULL,marker2label_angle=60,marker2label_size=2)

Error in snpgdsCreateGeno("test.gds", genmat = gene_snp2, sample.id = names(gene_snp)[12:dim(genesnp)[2]], : 'snpfirstdim=TRUE', but length(sample.id) is not the number of samples. In addition: There were 15 warnings (use warnings() to see them)

[whweve]

The errors may be resulted from the hapmap file format. As shown in the demo hapmap file, there are 11 columns before the columns corresponding to the sample name.

You may browse Vignette of IntAssoPlot by the command: browseVignettes("IntAssoPlot"). We have explained file format for each data required.

Your hapmap file dose not include a column "panel". So there are 10, not 11, colums before sample names in your dataset.

Hope that will be helpful

Hongwei Wang

Yangtzeu University

On 3/16/2021 22:37，Alisha @.***> wrote：

I have been trying to draw the plots but with eQTL variant P values from GTEx instead. I have the 1000G data converted to HapMap format and the association data contains the same columns as the example file provided, just the p-value is of an eQTL instead of a GWAS p-value. The annotation file was downloaded from Gencode.

I am just stuck due to multiple errors, the latest one being:

IntGenicPlot('ENST00000515776',gtf=gtf_hmgcr,association=association_hmgcr,hapmap=hapmap_hmgcr,

              hapmap_ld = NULL,threshold=NULL,up=100000,down=100000,leadsnpLD = FALSE,

              marker2highlight=NULL,link2gene=NULL,link2LD=marker2link,

             marker2label=NULL,marker2label_angle=60,marker2label_size=2)

Error in snpgdsCreateGeno("test.gds", genmat = gene_snp2, sample.id = names(gene_snp)[12:dim(genesnp)[2]], : 'snpfirstdim=TRUE', but length(sample.id) is not the number of samples. In addition: There were 15 warnings (use warnings() to see them)

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[alishaaman]

Hi Hongwei, Thanks a lot for the comments. I did rectify the columns and managed to generate the file, but with many warnings (all the same). I had used the gtf file from Ensembl http://ftp.ensembl.org/pub/release-103/gtf/homo_sapiens/ but am unable to get the exons and introns displayed - I have checked the file formats and attached it here (pic attached). Not quite sure what the issue is? This is only for the Genic plot. the regional plot seems to be drawn fine (but with the same warnings). All pictures attached. thanks

[whweve]

The question is resulted from your gtf file. There are no CDS in the V3 column.

IntAssoPlot plot exon as the background layer as a thin line, then put CDS as the upper layer as a wider line. Why we are doing this is because, exon may contain UTR, while CDS does not. If exon length is greater than CDS, and when exon and CDS are coloured differently, we can see where and length of UTR.

Suppose the gtf file dose not contain UTR, you can filter rows contain exon, and switch exon to CDS. Then, you can add the filtered file to your gtf file. By doing this, this question may be solved.

Let me know if you have any questions. Hongwei Wang

On 3/17/2021 17:16，Alisha @.***> wrote：

Hi Hongwei, Thanks a lot for the comments. I did rectify the columns and managed to generate the file, but with many warnings (all the same). I had used the gtf file from Ensembl http://ftp.ensembl.org/pub/release-103/gtf/homo_sapiens/ but am unable to get the exons and introns displayed - I have checked the file formats and attached it here (pic attached). Not quite sure what the issue is? This is only for the Genic plot. the regional plot seems to be drawn fine (but with the same warnings). All pictures attached. thanks

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