User: klkeysb

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klkeysb10
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Posts by klkeysb

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Answer: A: How to convert plink.raw to map and ped files in any software
... Possible solution [here][1]. Per Chris Chang's suggestion basically transpose the hard-called allele dosages (columns 6+ of PLINK RAW file) and stuff it through PLINK2 `--import-dosage`. KLK [1]: https://www.biostars.org/p/83681/#398262 ...
written 4 days ago by klkeysb10
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Answer: A: Plink Raw Format To Ped Format
... Leaving this here in case people still run into this problem. I implemented a suggestion from Chris Chang to beat a dosage file (subset of PLINK RAW) through a PLINK formatting pipeline. The output can be PED/MAP, BED/BIM/BAM, or whatever other PLINK output you like. See discussion [here][1]. KLK ...
written 4 days ago by klkeysb10
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Comment: C: Estimating required memory for WGCNA analysis
... I have seen that article before. The operative line is here: > 16 GB memory should be able to handle up to about 24,000 nodes; 32 GB should be enough (perhaps barely so) for 40,000 and so on. By that calculation, 80k transcripts require 64GB of memory. Imagine our surprise when moving to ~90k t ...
written 12 months ago by klkeysb10
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Estimating required memory for WGCNA analysis
... We are running WGCNA on ~90,000 genes in a single block with 48 threads and 192GB of memory using the `blockwiseModules` function. WGCNA takes several dozen hours to compute the topological overlap matrix. We thought that 192GB would be sufficient for the analysis. But WGCNA chokes when exporting ...
R wgcna rna-seq coexpression written 12 months ago by klkeysb10 • updated 12 months ago by Kevin Blighe48k

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