Error in genotypes[!blankSNPs, cox.params$ids] : subscript out of bounds

[hamishinnes]

Hi im trying to use gwasurvivr to run a survival analysis on plink data files.

the code im using is as follows:

plinkCoxSurv(bed.file="/users/ptb17163/lustre/EgaDemoClient_2.2.2/plink/top20variants.bed", covariate.file=df, covariates=c("age"), id.column="eid", time.to.event="X_t", event="fail", out.file="test",inter.term = NULL, print.covs = "only", chunk.size = 10000, verbose = TRUE, clusterObj = NULL )

however, when i run this, i get the following error message:

Error in genotypes[!blankSNPs, cox.params$ids] : subscript out of bounds

do you have any ideas as to what may be causing this - and how i can resolve it?

[aarizvi]

@hamishinnes -- can you verify that you your sample IDs match between your genotype columns and the covariate files sample IDs?

Are your sample IDs in your covariate file class character?

[hamishinnes]

problem solved!! my sample ID variable in my covariate was in a numeric format. I just converted it into character format, and it is now working perfectly. Thank you so much!!!! really great

[hamishinnes]

sorry that should have read... my sample ID variable in my covariate file was in a numeric format. I just converted it into character format, and it is now working perfectly. Thank you so much!!!!

[aarizvi]

Excellent. Let us know if you have any other issues. Closing this issue.

[karaesmen]

Great to hear! But we need to add a more sensible error message for this, I'd keep this issue open.

[syy525]

Hi, I'm trying to use gwasurvivr to run a survival analysis on impute2 data files.

The code I'm using is as follows:

impute2CoxSurv(impute.file=impute.file, sample.file=sample.file, chr=1, covariate.file=covariate.file, id.column="ID_1", sample.ids=sample.ids, time.to.event="timetoCRPC", event="Event1", covariates=c("age"), inter.term=NULL, print.covs="only", out.file="C:/Users/tomato/Desktop/chr1", chunk.size=100, maf.filter=0.005, exclude.snps=NULL, flip.dosage=TRUE, verbose=TRUE, clusterObj=NULL, keepGDS=FALSE)

However, when I run this, I got the following error message: * Compression time ** User:232.41 System: 18.85 Elapsed: 280.87

---

Analyzing part 1/17... Error in genotypes[, cox.params$ids] : subscript out of bounds

I read this article and I am sure my ID_1 and sample.ids are character; timetoCRPC, Event1, age are numbers. There is one possible reason that there are a lot of blanks (NA) in my covariate.file. I tried to fill them with numbers or NA or keep blanks, but the error is the same.

Do you have any ideas as to what may be causing this - and how can I resolve it?

[syy525]

Hi, I'm trying to use gwasurvivr to run a survival analysis on impute2 data files.

The code I'm using is as follows:

impute2CoxSurv(impute.file=impute.file, sample.file=sample.file, chr=1, covariate.file=covariate.file, id.column="ID_1", sample.ids=sample.ids, time.to.event="timetoCRPC", event="Event1", covariates=c("age"), inter.term=NULL, print.covs="only", out.file="C:/Users/tomato/Desktop/chr1", chunk.size=100, maf.filter=0.005, exclude.snps=NULL, flip.dosage=TRUE, verbose=TRUE, clusterObj=NULL, keepGDS=FALSE)

However, when I run this, I got the following error message: * Compression time ** User:232.41 System: 18.85 Elapsed: 280.87

Analyzing part 1/17... Error in genotypes[, cox.params$ids] : subscript out of bounds

I read this article and I am sure my ID_1 and sample.ids are character; timetoCRPC, Event1, age are numbers. There is one possible reason that there are a lot of blanks (NA) in my covariate.file. I tried to fill them with numbers or NA or keep blanks, but the error is the same.

Do you have any ideas as to what may be causing this - and how can I resolve it?

I would like to add that, I tried the example from your website: n100_p1000_chr18 (.impute), n100.impute_sample (.txt), simulated_pheno (.txt) and met the same errors.

However, when I changed the n100.impute_sample (.txt) to impute_example.IMPUTE2_SAMPLE, it could run perfectly.

I wonder if the problem is due to sample file could not be .txt!!? And it should be .sample or .IMPUTE2_SAMPLE.

[aarizvi]

Very interesting indeed. Those files should be fine as .txt or any extension as long as they are tab separated.

And although you said it's not the case -- the error from your first post -- looks like a sampleID issue. Can you do class() on that column and paste it here?

[syy525]

Very interesting indeed. Those files should be fine as .txt or any extension as long as they are tab separated.

And although you said it's not the case -- the error from your first post -- looks like a sampleID issue. Can you do class() on that column and paste it here?

Below is the class() data:

class(sample.ids) [1] "character" class(covariate.file$ID_1) [1] "character" class(covariate.file$ID_2) [1] "character" class(covariate.file$Event1) [1] "numeric" class(covariate.file$timetoCRPC) [1] "numeric" class(covariate.file$age) [1] "numeric"

By the way, there are 1037 objects in my study and 422 objects were picked up in sample.ids. And the error showed: Analyzing part 1/1613... Error in genotypes[, cox.params$ids] : subscript out of bounds

Why there are part 1/1613 in my study? Should it be 1/422?

Many thanks.

[aarizvi]

Because these data are large and R may be overloaded by very large matrices, we chunk up the genotype matrix. Thats why you have 1613 parts. It doesnt have to do with your sampleIDs.

The next step I would suggest is to actually load in the genotype data into R (perhaps maybe like the first 5 rows) and confirm that the column headers of your genotype matrix are the same names as your sample IDs.

Something like ...

table(colnames(genotype_matrix) %in% covariate.file$ID_1)

[syy525]

table(colnames(genotype_matrix) %in% covariate.file$ID_1)

My genotype file is from IMPUTE2, there is no header on it. So the code "table(colnames(genotype_matrix) %in% covariate.file$ID_1)" showed FALSE 3116

When my "genotype file" was imported into R using read.table, It look like: V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13.... --- 1:10177:A:AC 10177 A AC 0.379 0.482 0.138 0.208 0.651 0.141 0.672 0.303 ...

The sample.file look like: ID_1 ID_2 missing sex 1 0 0 0 D 2 2 38509_2 0 1 3 3 38201_2 0 1 4 4 38728_2 0 1 5 5 38371_2 0 1 6 6 38397_2 0 1

The covariate.file look like: ID_1 ID_2 Event1 timetoCRPC age Mstage GSabove7 1 2 38509_2 0 125 67 0 0 2 3 38201_2 0 125 67 0 0 3 4 38728_2 0 125 67 0 0 4 5 38371_2 0 125 67 0 0 5 6 38397_2 0 125 67 0 0 6 7 38414_2 0 125 67 0 0

Is there anything wrong with these?

[aarizvi]

Everything arguably looks good besides the genotype file.

You need to add a header ... to the genotype file. the first 7 columns should be something like

first_seven <- c("snpID", "TYPED", "RSID", "POS", "A0", "A1", "CHR"))

From column 8 on, the column names need to be the same as your sampleIDs. So in your case it would be colnames(genotypes) <- c(first_seven, 1:(ncol(genotypes)-7))

However, I would suggest changing your sample names to something likepaste0("samp", 1:nrow(sample.file)). But keep in mind, you'd have to follow the same schema for sample.file, covariate.file, and genotype.

And the reason for changing the names -- is so you have characters are column names for the genotype file instead of numerics. It makes it less prone to error. But should work either way.

[syy525]

Interestingly, my team found the problem. The error was not due to genotype file of mine, which is the same format as the "gwasurvivr example: n100_p1000_chr18.impute". It really do not need header. snp_0 18-221 221 C T 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0.......(n100_p1000_chr18.impute)

The problem is still due to ""sample file". my sample.file look like: ID_1 ID_2 missing sex 0 0 0 D 2 38509_2 0 1 3 38201_2 0 1 4 38728_2 0 1 5 38371_2 0 1 6 38397_2 0 1

The ID_1 is different from ID_2. When we made them the same, it could run perfectly, ID_1 ID_2 missing sex 0 0 0 D 2 2 0 1 3 3 0 1 4 4 0 1 5 5 0 1 6 6 0 1

Go back to the script, we guest it might be due to the effect of this command which using ID_2.

and sample ID as columns to genotype file

    dimnames(genotypes) <- list(paste(snp$TYPED, snp$RSID, sep=";"), 
                                scanAnn$ID_2)

Thank you for all of your reply, this is a great software to run GWAS survival!!!!

[Qiaolan]

Interestingly, my team found the problem. The error was not due to genotype file of mine, which is the same format as the "gwasurvivr example: n100_p1000_chr18.impute". It really do not need header. snp_0 18-221 221 C T 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0.......(n100_p1000_chr18.impute)

The problem is still due to ""sample file". my sample.file look like: ID_1 ID_2 missing sex 0 0 0 D 2 38509_2 0 1 3 38201_2 0 1 4 38728_2 0 1 5 38371_2 0 1 6 38397_2 0 1

The ID_1 is different from ID_2. When we made them the same, it could run perfectly, ID_1 ID_2 missing sex 0 0 0 D 2 2 0 1 3 3 0 1 4 4 0 1 5 5 0 1 6 6 0 1

Go back to the script, we guest it might be due to the effect of this command which using ID_2.

and sample ID as columns to genotype file

dimnames(genotypes) <- list(paste(snp$TYPED, snp$RSID, sep=";"), scanAnn$ID_2)

Thank you for all of your reply, this is a great software to run GWAS survival!!!!

The same issue happened to me. FID did not work, but IID worked well.

[tesselgalesloot]

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