samples IDs in plink.mdist.missing file

[Denis]

Hi,

I used "--cluster missing" option in PLINK 1.9, but there are no sample names in the "plink.mdist.missing" file.

According to the documentation : ".cluster3[.missing] files contain one line per sample, with their FID and IID as the first two fields (not merged with an underscore here), followed by a sequence of nonnegative integers representing the sample's cluster assignment at each stage of the clustering process."

Why i have not sample names in my case and how can i add them to the my "plink.mdist.missing" file? I need that to visualize the distances in R environment.

Regards,

Denis

[Christopher Chang]

Please post a full .log file, and preferably also the input files used in the run (these could be small, as long as they illustrate the issue you're having).

[Denis]

Hi,

Thanks for your reply. The  "plink.mdist.missing" file is a matrix :

".mdist.missing (identity-by-missingness matrix)

Produced by "--cluster missing".

A triangular space-delimited text file with identity-by-missingness coefficients."

But without sample IDs available as a column and row names of the matrix it is not possible to correctly interpret and visualize IBM distances between samples. How can i get the same file, but with sample IDs for further analysis of the matrix?

The log file is:

"

PLINK v1.90b6.26 64-bit (2 Apr 2022)
Options in effect:
  --allow-extra-chr
  --cluster missing
  --keep-allele-order
  --vcf Diploids_GBS.vcf

Hostname: node03
Working directory: /mnt/lustre/tkiy/Diploids_GBS/GBS_pipeline
Start time: Fri May  6 15:44:17 2022

Random number seed: 1651841057
48258 MB RAM detected; reserving 24129 MB for main workspace.
--vcf: plink-temporary.bed + plink-temporary.bim + plink-temporary.fam written.
109444 variants loaded from .bim file.
96 people (0 males, 0 females, 96 ambiguous) loaded from .fam.
Ambiguous sex IDs written to plink.nosex .
Using up to 23 threads (change this with --threads).
Before main variant filters, 96 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.476451.
109444 variants and 96 people pass filters and QC.
Note: No phenotypes present.
IBM matrix written to plink.mdist.missing .
Clustering... done.
Cluster solution written to plink.cluster1 , plink.cluster2 , and
plink.cluster3.missing .

"

Please let me know if my VCF file is still needed to replicate the issue. I'll try to prepare a toy example of my VCF for sending in that case.

Regards,

Denis

пятница, 6 мая 2022 г. в 18:11:14 UTC+3, chrch...@gmail.com:

[Christopher Chang]

Oh, this isn't built into plink 1.x, sorry.  You should use a short shell script that reads the sample IDs from the .fam file and attaches them to the .mdist.missing file in the manner you prefer.

[Denis]

Thank you! I'm wondering if i'd get a correct matrix (with column and row names) using PLINK 1.07?

Regards,

Denis

пятница, 6 мая 2022 г. в 19:44:44 UTC+3, chrch...@gmail.com:

[Christopher Chang]

"plink 1.x" means plink 1.07 has the same behavior.

[Christopher Chang]

(Note that, because of plink 1.x's two-part sample IDs, there is no obvious way to define what you're calling a "correct matrix".)

On Friday, May 6, 2022 at 9:56:15 AM UTC-7 Denis wrote:

[Denis]

Is the IDs order in the "plink.cluster3.missing" ( the first two fields ) and  "plink.mdist.missing" files identical? May i just coppy these and paste to the  "plink.mdist.missing" file? Could you confirm that please?

Regards,

Denis

пятница, 6 мая 2022 г. в 20:01:12 UTC+3, chrch...@gmail.com:

[Christopher Chang]

Yes, the order is the same.

[Denis]

Thank you so much for the clarification!

Best,

Denis

пятница, 6 мая 2022 г. в 20:43:30 UTC+3, chrch...@gmail.com: