Moderator: zx8754

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zx87549.3k
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"If you torture the data long enough, it will confess." - Ronald Coase

Posts by zx8754

<prev • 1,106 results • page 1 of 111 • next >
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Answer: A: PED file PLINK
... It is [Irregularly-formatted PLINK text files](https://www.cog-genomics.org/plink/1.9/input), using below flags that ped file should work fine: plink --file myFile --no-fid --no-parents --no-sex --no-pheno --make-bed --out myFileBinary ...
written 4 days ago by zx87549.3k
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Comment: C: Exporting files from Plink with sample IDs?
... Since you are using `--tfile` flag, then you must have *examplesnps.tped* and *examplesnps.tfam* (which has the same format as [.fam file](https://www.cog-genomics.org/plink/1.9/formats#fam)). That tfam file would have the sample IDs. ...
written 5 days ago by zx87549.3k
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Comment: C: GSEA for genes in R
... Maybe just make your own set of genes? Doesn't have to a be a pathway. There are many R packages, here is one from Bioconductor: - https://bioconductor.org/packages/release/bioc/html/GSEABase.html ...
written 5 days ago by zx87549.3k
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Answer: A: How to combine two networks
... Using **R** igraph union: library(igraph) net1 <- graph_from_literal(A-B:C:D, A-C, B-C) net2 <- graph_from_literal(A-X:Y:Z, Z-Y) par(mfrow = c(1, 3)) set.seed(1) plot(net1, vertex.size = 50, main = "net1") plot(net2, vertex.size = 50, main = "net2") p ...
written 8 days ago by zx87549.3k
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Comment: C: Change the field separator
... Maybe read the manual for **sed**? https://en.wikipedia.org/wiki/Sed ...
written 10 days ago by zx87549.3k
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Answer: A: Change the field separator
... Using **R**, just read the file with *sep*: read.table("myFile.txt", sep = "/") # V1 V2 V3 V4 V5 V6 V7 V8 #1 CG10226 CG33120 RyR Tsp42Eg CG1234 Act57B Apoltp CG9194 ...
written 10 days ago by zx87549.3k
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Answer: A: Extracting strings from the fasta header
... Here is the start: # example data x <- c("lcl|NC_005336.1_cds_NP_957781.1_1 [locus_tag=ORFVgORF001] [db_xref=GeneID:2947687] [protein=ORF001 hypothetical protein] [protein_id=NP_957781.1] [location=complement(3162..3611)] [gbkey=CDS]", "lcl|NC_001111_NP_999_1 [locus_tag=Test00 ...
written 18 days ago by zx87549.3k
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Comment: C: DeSeq2 error: counts matrix should be numeric, currently it has mode: character
... `cts` object is not numeric, could you paste the output of `cts[1:10, 1:10]` ? ...
written 6 weeks ago by zx87549.3k
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Comment: C: Warning: Error in fread: is.logical(header) && length(header) == 1L is not TRUE
... This is more relevant as an issue at GitHub: - https://github.com/honzee/RNAseqCNV/issues ...
written 7 weeks ago by zx87549.3k
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Comment: C: file conversion in bash
... As mentioned csv is already a plain text format with "," or ";" as a separator. Two options: 1. replace the comma with another separator of your choice, [for example by using tr](https://unix.stackexchange.com/a/87447/16560) 2. just rename the extension: `mv myfile.csv myfile.txt`. ...
written 9 weeks ago by zx87549.3k

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