Error in (function (cl, name, valueClass) : assignment of an object of class “NULL” is not valid for @‘i’ in an object of class “dsCMatrix”; is(value, "integer") is not TRUE

[Mahantesh-Biradar]

I'm getting the following error, when I tried to run the calculate LD step.

My code:

# calculate LD
for (chr in 1:22) {
  # Extract SNPs that are included in the chromosome
  ind.chr <- which(info_snp$chr == chr)
  ind.chr2 <- info_snp$`_NUM_ID_`[ind.chr]
  # Calculate the LD
  corr0 <- snp_cor(
    genotype2,
    ind.col = ind.chr2,
    ncores = NCORES,
    infos.pos = POS2[ind.chr2],
    size = 3 / 1000
  )
  if (chr == 1) {
    ld <- Matrix::colSums(corr0^2)
    corr <- as_SFBM(corr0, tmp)
  } else {
    ld <- c(ld, Matrix::colSums(corr0^2))
    corr$add_columns(corr0, nrow(corr))
  }
}

Error:

Error in (function (cl, name, valueClass)  : 
  assignment of an object of class “NULL” is not valid for @‘i’ in an object of class “dsCMatrix”; is(value, "integer") is not TRUE

Can you please suggest how I can address this error? TIA

[privefl]

It's almost as if there is no data in corr0. What is the size of these sparse matrices?

[Mahantesh-Biradar]

dim(corr0) NULL

I'm not sure why this is happening?

[privefl]

Check ind.chr and ind.chr2 I guess

[Mahantesh-Biradar]

dim(ind.chr) NULL dim(ind.chr2) NULL

[privefl]

It's normal since these are vectors. Look at the length.

[Mahantesh-Biradar]

length(ind.chr) [1] 0 length(ind.chr2) [1] 0

[privefl]

Yes, that's definitely the issue. You should check your code.

[Mahantesh-Biradar]

Can you please suggest, which step in the code be causing this issue?

[privefl]

You need to check why you get no index when running ind.chr <- which(info_snp$chr == chr).

[Mahantesh-Biradar]

I tend to have issues like this when the software version is updated. Can you please tell me how I can switch back to 1.12.1 from 1.12.2?

Let me also try your suggestion.

[Mahantesh-Biradar]

Hi Florian,

The info and info_snp looks as follows:

info: chr pos a0 a1 rsid af_UKBB ld block_id pos_hg18 pos_hg38

1 1 68082 T C rs367789441 0.0708 1.81 1 57945 68082 2 1 77866 C T rs563593912 0.0769 1.30 1 67729 77866 3 1 87409 C T rs139490478 0.0768 1.57 1 77272 87409 info_snp: info_snp chr pos a0 a1 rsid.ss CHR:BP_A1_A2 Z n_eff MAF beta beta_se mtag_z p 1 1 1229680 T G rs2477781 1:1229680_G_T 1.36363636 139555 0.9543 7.483735e-03 0.008507473 0.879665945 3.790403e-01 2 1 1231656 G A rs1749951 1:1231656_G_A 0.11232877 139555 0.0378 -6.861773e-03 0.009315852 0.736569550 4.613842e-01 3 1 1239847 C T rs77641120 1:1239847_C_T 2.03218391 139555 0.0149 -2.646836e-02 0.014664521 1.804925040 7.108641e-02 4 1 1241529 G A rs1536168 1:1241529_A_G -0.11918605 139555 0.9553 -6.278337e-03 0.008597605 -0.730242521 4.652420e-01

[privefl]

You should check your code by yourself, I can't help you more with this. This is not an issue on my part. E.g. do you know for which chromosome the problem occurs? Why? Do you have an issue with how chromosomes are labelled? How many variants are matched?

[Mahantesh-Biradar]

Thanks. In my summary stats I had about 12K variants and around 11K are matched. I'm not sure which chromosome is causing the issue.

[privefl]

table(info_snp$chr)

[privefl]

Sumstats with only 12K variants is odd.

[Mahantesh-Biradar]

Thanks for your help again. I agree, I have filtered my summary stats file to include only a selected SNPs.

table(info_snp$chr)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22 1122 987 1492 343 639 364 358 628 238 356 574 406 125 700 190 576 781 59 562 179 430

[privefl]

You don't have anything from chr 21..

[Mahantesh-Biradar]

Thanks Florian. I think that address the issue. Going to close this now!