Error in ld(): STRING_ELT() can only be applied to a 'character vector', not a 'NULL'
Entering edit mode
Anastasiia • 0
Last seen 5 weeks ago

Hi all,

I am trying to calculate linkage disequilibrium using snpStats function ld()

But I keep receiving errors of all sorts. Below are 2 of my attempts to produce any result and the following errors

I don't know how to approach this problem

Thank you in advance


SNPMatrix <- read.plink('Ia.bed', 'a.bim', 'a.fam', sep= ".") 

# 1
LD_matrix <- ld(SNPMatrix, y = SNPMatrix, stats = "R.squared", symmetric = TRUE)
Error in ld(SNPMatrix, y = SNPMatrix, stats = "R.squared", symmetric = TRUE) : 
  STRING_ELT() can only be applied to a 'character vector', not a 'NULL'

LD_matrix <- ld(SNPMatrix, depth = 100, stats = "R.squared") 
Error in if (depth > dmax) { : argument is of length zero

sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=pl_PL.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=pl_PL.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=pl_PL.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=pl_PL.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] snpStats_1.44.0 Matrix_1.3-4    survival_3.2-13 LDheatmap_1.0-4

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7          pillar_1.6.4        compiler_4.1.2      zlibbioc_1.40.0     prettyunits_1.1.1   remotes_2.4.2       tools_4.1.2         testthat_3.1.0     
 [9] pkgbuild_1.2.1      pkgload_1.2.4       lattice_0.20-45     memoise_2.0.1       lifecycle_1.0.1     tibble_3.1.6        pkgconfig_2.0.3     rlang_0.4.12       
[17] rstudioapi_0.13     DBI_1.1.1           cli_3.1.0           curl_4.3.2          fastmap_1.1.0       withr_2.4.3         dplyr_1.0.7         generics_0.1.1     
[25] desc_1.4.0          fs_1.5.1            vctrs_0.3.8         devtools_2.4.3      grid_4.1.2          rprojroot_2.0.2     tidyselect_1.1.1    glue_1.5.1         
[33] R6_2.5.1            processx_3.5.2      fansi_0.5.0         sessioninfo_1.2.1   callr_3.7.0         purrr_0.3.4         magrittr_2.0.1      BiocGenerics_0.40.0
[41] splines_4.1.2       ps_1.6.0            ellipsis_0.3.2      usethis_2.1.3       assertthat_0.2.1    utf8_1.2.2          cachem_1.0.6        crayon_1.4.2
ld() snpStats • 120 views
Entering edit mode

Can you confirm that SNPMatrix has been read correctly & contains the sort of data you're expecting? Perhaps check dim(SNPMatrix) and head(SNPMatrix) to confirm it looks ok.

Does the example from the ?ld manual page work for you?

ld1 <- ld(Autosomes[, 1:50], depth=10, stats=c("", "R.squared"))
ld2 <- ld(Autosomes[, 1:20], Autosomes[, 21:25], stats="R.squared")
Entering edit mode

Hi, thank you for replying!

Examples work perfectly but I saw, that testdata doesn't look like my input data, I just wonder why those are 2 dataframes and not a SnpMatrix object

Anyways, when I try reading my files

SNPMatrix <- read.plink('a.bed', 'a.bim', 'a.fam', sep= ".")

it produces a large list of 3 elements






$genotypes A SnpMatrix with 240 rows and 54209 columns Row names: AAS10 ... TRE9 Col names: IpsContig13_4598 ... IpsContig13_5972420

$fam pedigree member father mother sex affected AAS10 AAS10 AAS10 NA NA NA NA AAS18 AAS18 AAS18 NA NA NA NA AAS2 AAS2 AAS2 NA NA NA NA

SIL2-6 SIL2-6 SIL2-6 NA NA NA NA [ reached 'max' / getOption("max.print") -- omitted 74 rows ]

$map chromosome cM position allele.1 allele.2 IpsContig13_4598 IpsContig13 IpsContig13_4598 NA 4598 T A IpsContig13_4658 IpsContig13 IpsContig13_4658 NA 4658 C T IpsContig13_5091 IpsContig13 IpsContig13_5091 NA 5091 A G

[ reached 'max' / getOption("max.print") -- omitted 54043 rows ]

Sorry for the awkward output format, I also cut it for simplicity
So, read.plink does read my data somehow, but I can't be sure if everything is alright


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