Arguments imply differing number of rows

[parvathisudha]

Hi,

When I use dNdScv, I am getting this error. This happens only for few samples. I couldn't find any issue with the sample file. All the samples has ID, chr, pos, ref and alt. Can you please tell me how to solve this error?

> dndsout_all = dndscv(smm_var, refdb = "RefCDS_human_GRCh38_GencodeV18_recommended.rda", cv = "covariates_hg19_hg38_epigenome_pcawg.rda",max_muts_per_gene_per_sample = Inf, max_coding_muts_per_sample = Inf) [1] Loading the environment... [2] Annotating the mutations... [3] Estimating global rates... [4] Running dNdSloc... [5] Running dNdScv... Regression model for substitutions (theta = 1.71). Error in data.frame(gene_name = genemuts$gene_name, n_syn = genemuts$n_syn, : arguments imply differing number of rows: 19216, 0, 1 In addition: Warning messages: 1: In data(list = sprintf("covariates_%s", cv), package = "dndscv") : data set ?covariates_covariates_hg19_hg38_epigenome_pcawg.rda? not found 2: In dndscv(smm_var, refdb = "RefCDS_human_GRCh38_GencodeV18_recommended.rda", : Mutations observed in contiguous sites within a sample. Please annotate or remove dinucleotide or complex substitutions for best results. 3: In dndscv(smm_var, refdb = "RefCDS_human_GRCh38_GencodeV18_recommended.rda", : Same mutations observed in different sampleIDs. Please verify that these are independent events and remove duplicates otherwise. 4: In model$y == genemuts$n_syn : longer object length is not a multiple of shorter object length

Thanks Parvathi.

[im3sanger]

Hi Parvathi,

Thanks for your interest in dndscv. Could you send me a small example dataset that reproduces this error (through this chat or by email)? I have never come across it before.

Best, Inigo

[parvathisudha]

Hi,

Thanks for your reply. I am attaching variants for one of the samples to this email. I have a few more samples like this. Please let me know if you find any problem in this file.

Thanks Parvathi.

On Thu, Mar 2, 2023 at 10:08 PM Inigo Martincorena @.***> wrote:

Hi Parvathi,

Thanks for your interest in dndscv. Could you send me a small example dataset that reproduces this error (through this chat or by email)? I have never come across it before.

Best, Inigo

— Reply to this email directly, view it on GitHub https://github.com/im3sanger/dndscv/issues/86#issuecomment-1452174542, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADDGAL2XXWBIOOV5GXKRVGDW2DEJFANCNFSM6AAAAAAVMRWNYA . You are receiving this because you authored the thread.Message ID: @.***>

--

Thanks

Parvathi Sudha.

SampleID chr pos ref alt 0661-619_4410453_T 1 839489 G A 0661-619_4410453_T 1 839499 A T 0661-619_4410453_T 1 988598 A G 0661-619_4410453_T 1 1384749 C G 0661-619_4410453_T 1 1548572 A C 0661-619_4410453_T 1 1612560 G T 0661-619_4410453_T 1 1928114 A T 0661-619_4410453_T 1 2659557 A G 0661-619_4410453_T 1 2677361 T A 0661-619_4410453_T 1 2695843 T C 0661-619_4410453_T 1 2849107 A G 0661-619_4410453_T 1 2852084 A G 0661-619_4410453_T 1 2852092 T C 0661-619_4410453_T 1 2866866 T G 0661-619_4410453_T 1 2880595 G A 0661-619_4410453_T 1 3163341 A G 0661-619_4410453_T 1 3287837 C G 0661-619_4410453_T 1 3299300 A G 0661-619_4410453_T 1 3428319 A G 0661-619_4410453_T 1 3524700 G A 0661-619_4410453_T 1 3583340 G C 0661-619_4410453_T 1 3722904 A G 0661-619_4410453_T 1 3729861 G A 0661-619_4410453_T 1 3813025 A G 0661-619_4410453_T 1 4369080 A G 0661-619_4410453_T 1 4455174 C G 0661-619_4410453_T 1 4516779 C T 0661-619_4410453_T 1 5203784 A G 0661-619_4410453_T 1 5740844 G A 0661-619_4410453_T 1 6307819 T A 0661-619_4410453_T 1 6714516 A T 0661-619_4410453_T 1 6834156 T A 0661-619_4410453_T 1 7156130 T A 0661-619_4410453_T 1 7746615 C T 0661-619_4410453_T 1 7877148 A G 0661-619_4410453_T 1 8456797 T A 0661-619_4410453_T 1 8498770 T C 0661-619_4410453_T 1 8974600 C T 0661-619_4410453_T 1 9624608 G A 0661-619_4410453_T 1 9969672 A G 0661-619_4410453_T 1 10188959 A T 0661-619_4410453_T 1 10223555 T G 0661-619_4410453_T 1 10871567 T C 0661-619_4410453_T 1 11903310 C G 0661-619_4410453_T 1 12203737 T A 0661-619_4410453_T 1 13006045 G A 0661-619_4410453_T 1 13070265 T C 0661-619_4410453_T 1 13224737 G C 0661-619_4410453_T 1 13243400 C T 0661-619_4410453_T 1 13251521 G A 0661-619_4410453_T 1 13260152 C A 0661-619_4410453_T 1 13334006 A G 0661-619_4410453_T 1 13432421 G C 0661-619_4410453_T 1 13461564 T C 0661-619_4410453_T 1 14152728 A G 0661-619_4410453_T 1 14177798 T G 0661-619_4410453_T 1 15027903 G A 0661-619_4410453_T 1 15367840 C T 0661-619_4410453_T 1 15369130 A T 0661-619_4410453_T 1 15667219 T A 0661-619_4410453_T 1 15790503 A C 0661-619_4410453_T 1 16426583 T A 0661-619_4410453_T 1 16532015 T A 0661-619_4410453_T 1 16551624 C T 0661-619_4410453_T 1 16551626 C T 0661-619_4410453_T 1 16551736 C G 0661-619_4410453_T 1 16557798 G A 0661-619_4410453_T 1 16561095 C A 0661-619_4410453_T 1 16561428 G A 0661-619_4410453_T 1 16610876 T C 0661-619_4410453_T 1 16626269 A C 0661-619_4410453_T 1 16644329 G T 0661-619_4410453_T 1 16644788 T G 0661-619_4410453_T 1 16755215 G C 0661-619_4410453_T 1 16760375 T C 0661-619_4410453_T 1 16850197 G A 0661-619_4410453_T 1 16860028 G A 0661-619_4410453_T 1 16862959 G A 0661-619_4410453_T 1 16868017 G A 0661-619_4410453_T 1 17450178 A C 0661-619_4410453_T 1 17674732 C T 0661-619_4410453_T 1 19351979 A C 0661-619_4410453_T 1 19495302 T A 0661-619_4410453_T 1 21020735 A C 0661-619_4410453_T 1 21041008 G A 0661-619_4410453_T 1 21341034 A C 0661-619_4410453_T 1 21484082 T C 0661-619_4410453_T 1 21588771 T G 0661-619_4410453_T 1 21903053 C G 0661-619_4410453_T 1 22005826 G A 0661-619_4410453_T 1 22005840 G A 0661-619_4410453_T 1 22231211 A C 0661-619_4410453_T 1 22681197 C T 0661-619_4410453_T 1 23585035 T C 0661-619_4410453_T 1 23758264 T A 0661-619_4410453_T 1 23758268 T A 0661-619_4410453_T 1 23837673 T G 0661-619_4410453_T 1 24159736 T G 0661-619_4410453_T 1 24159737 G T 0661-619_4410453_T 1 24219309 C T 0661-619_4410453_T 1 25091472 C T 0661-619_4410453_T 1 25178007 G A 0661-619_4410453_T 1 25214741 A T 0661-619_4410453_T 1 25679978 T C 0661-619_4410453_T 1 26282398 A T 0661-619_4410453_T 1 26811571 C T 0661-619_4410453_T 1 26951932 C T 0661-619_4410453_T 1 27107482 C A 0661-619_4410453_T 1 27985262 C A 0661-619_4410453_T 1 28860363 A T 0661-619_4410453_T 1 29581739 C T 0661-619_4410453_T 1 29931761 C A 0661-619_4410453_T 1 30191452 G A 0661-619_4410453_T 1 30478728 A C 0661-619_4410453_T 1 30818871 C G 0661-619_4410453_T 1 30832799 G A 0661-619_4410453_T 1 31449998 A T 0661-619_4410453_T 1 32061900 T C 0661-619_4410453_T 1 32198058 A G 0661-619_4410453_T 1 32208265 G C 0661-619_4410453_T 1 32827786 T G 0661-619_4410453_T 1 32841175 T A 0661-619_4410453_T 1 32933271 G T 0661-619_4410453_T 1 33148658 G A 0661-619_4410453_T 1 35267859 A C 0661-619_4410453_T 1 35268545 G C 0661-619_4410453_T 1 36014798 A G 0661-619_4410453_T 1 36022933 C A 0661-619_4410453_T 1 36295238 A G 0661-619_4410453_T 1 36736168 G A 0661-619_4410453_T 1 37332944 A G 0661-619_4410453_T 1 37685383 T C 0661-619_4410453_T 1 37695192 T A 0661-619_4410453_T 1 37863219 A T 0661-619_4410453_T 1 38005756 A C 0661-619_4410453_T 1 38039805 G A 0661-619_4410453_T 1 38434064 G A 0661-619_4410453_T 1 38460222 G A 0661-619_4410453_T 1 38571775 C A 0661-619_4410453_T 1 38683534 G T 0661-619_4410453_T 1 38865862 G A 0661-619_4410453_T 1 38874331 A T 0661-619_4410453_T 1 38875643 G T 0661-619_4410453_T 1 38931541 A G 0661-619_4410453_T 1 39381378 T G 0661-619_4410453_T 1 39393196 A T 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0661-619_4410453_T 3 12978094 G A 0661-619_4410453_T 3 13765485 G A 0661-619_4410453_T 3 14264720 G C 0661-619_4410453_T 3 15514112 T C 0661-619_4410453_T 3 16084507 A T 0661-619_4410453_T 3 16203545 A T 0661-619_4410453_T 3 16401324 A C 0661-619_4410453_T 3 16707998 G A 0661-619_4410453_T 3 16937067 A G 0661-619_4410453_T 3 19070372 T C 0661-619_4410453_T 3 19074615 A T 0661-619_4410453_T 3 19381832 C T 0661-619_4410453_T 3 19596149 G A 0661-619_4410453_T 3 20097240 G A 0661-619_4410453_T 3 20591648 C A 0661-619_4410453_T 3 20595927 C A 0661-619_4410453_T 3 20606223 G A 0661-619_4410453_T 3 20855431 T C 0661-619_4410453_T 3 20943956 A G 0661-619_4410453_T 3 21083175 G T 0661-619_4410453_T 3 21193035 G A 0661-619_4410453_T 3 23284511 A T 0661-619_4410453_T 3 24009017 C T 0661-619_4410453_T 3 24613766 G T 0661-619_4410453_T 3 24664327 T C 0661-619_4410453_T 3 24930327 C T 0661-619_4410453_T 3 24991318 C T 0661-619_4410453_T 3 25157378 G A 0661-619_4410453_T 3 26136412 T C 0661-619_4410453_T 3 26280824 A T 0661-619_4410453_T 3 26309296 C T 0661-619_4410453_T 3 26603630 G A 0661-619_4410453_T 3 27678716 G A 0661-619_4410453_T 3 27784945 T A 0661-619_4410453_T 3 27954782 T C 0661-619_4410453_T 3 28676708 C T 0661-619_44104

[parvathisudha]

Hi Inigo,

Were you able to reproduce the same error using this sample file? Please let me know how to proceed with this sample.

Thanks! Parvathi.

On Wed, Mar 8, 2023 at 12:31 AM Parvathi Kk @.***> wrote:

Hi,

Thanks for your reply. I am attaching variants for one of the samples to this email. I have a few more samples like this. Please let me know if you find any problem in this file.

Thanks Parvathi.

On Thu, Mar 2, 2023 at 10:08 PM Inigo Martincorena < @.***> wrote:

Hi Parvathi,

Thanks for your interest in dndscv. Could you send me a small example dataset that reproduces this error (through this chat or by email)? I have never come across it before.

Best, Inigo

— Reply to this email directly, view it on GitHub https://github.com/im3sanger/dndscv/issues/86#issuecomment-1452174542, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADDGAL2XXWBIOOV5GXKRVGDW2DEJFANCNFSM6AAAAAAVMRWNYA . You are receiving this because you authored the thread.Message ID: @.***>

--

Thanks

Parvathi Sudha.

--

Thanks

Parvathi Sudha.

[parvathisudha]

Hi,

I solved this issue by generating the reference with the genome file used for processing the sample.
Use buildref()

Thanks Parvathi.

[z1242099843]

I also encountered this problem, and I built the reference data of hg38 by myself, but still the same error occurs。

[1] Loading the environment... [2] Annotating the mutations... [3] Estimating global rates... [4] Running dNdSloc... [5] Running dNdScv... Regression model for substitutions (theta = 1.86). Error in data.frame(gene_name = genemuts$gene_name, n_syn = genemuts$n_syn, : 参数值意味着不同的行数: 19216, 0, 1 In addition: Warning messages: 1: In dndscv(a, refdb = refdb, use_indel_sites = T, min_indels = 1, : Mutations observed in contiguous sites within a sample. Please annotate or remove dinucleotide or complex substitutions for best results. 2: In dndscv(a, refdb = refdb, use_indel_sites = T, min_indels = 1, : Same mutations observed in different sampleIDs. Please verify that these are independent events and remove duplicates otherwise. 3: In model$y == genemuts$n_syn : longer object length is not a multiple of shorter object length

I would like to know why this error occurs and how to fix it.

[parvathisudha]

Hi,

The code I used:

`library("dndscv")

path_cds_table = "./Hg38_cds_mart_export.txt"

path_genome_fasta = "./GRCh38.primary_assembly.genome.fa"

buildref(cdsfile=path_cds_table, genomefile=path_genome_fasta, outfile = "Hg38_output_refcds.rda", excludechrs="MT", useids = T)

all <- read.table(file = "./All_variants.txt", sep ="\t", header = T)

dndsout = dndscv(all, refdb = "Hg38_output_refcds.rda", cv=NULL,max_muts_per_gene_per_sample = Inf, max_coding_muts_per_sample = Inf) ` Thanks! -Parvathi.

[AnthonyShea1]

Hi Parvathi,

I am running into the same problem as you.

I am curious where you downloaded your "GRCh38.primary_assembly.genome.fa" file.

I have tried using the ensemble hg38 primary assembly (https://ftp.ensembl.org/pub/release-102/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz), however I run into the issue described in issue #55.

> buildref(cdsfile=path_cds_table, genomefile=path_genome_fasta, 
+          outfile = "Hg38.rda", excludechrs="MT", useids = T)
[1/3] Preparing the environment...
[2/3] Building the RefCDS object...
Error in gene_split[[j]] : subscript out of bounds

The suspected reason is due to the presence of padded N's in my reference:

chr1 1 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Thanks, Anthony.

[im3sanger]

Hello,

Please accept my apologies for the silence.

I would like to understand this error better, as you should not need to regenerate the hg38 object. I would recommend using the hg38 RefCDS and covariates objects provided in the dndscv_data package instead.

Anthony, could you send me a small example file of mutations that reproduces the error? I will try to look into this if I can reproduce it.

Many thanks and sorry, Parvathi, for not acting on this sooner, Inigo

PS. I also just noticed that one of the warnings in Parvathi's first message said that the covariates were not recognised. This was due to input the filename for the covariates in the cv argument. Instead you need to load the covariates and input them as a matrix, as in the example below:

load("covariates_hg19_hg38_epigenome_pcawg.rda") # Loads the covs object
dndsout = dndscv(mutations, refdb = "RefCDS_human_GRCh38_GencodeV18_recommended.rda", cv = covs)

[AnthonyShea1]

Hi Inigo,

Thanks for the quick response. Loading the covariates fixed the Issue!

Appreciate the help!