Moderator: zx8754

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zx87547.8k
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"If you torture the data long enough, it will confess." - Ronald Coase

Posts by zx8754

<prev • 910 results • page 1 of 91 • next >
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Comment: C: Ordering of rowVar in drawing Heatmap
... See: https://www.biostars.org/p/309884/ and edit your post with images. ...
written 2 days ago by zx87547.8k
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Answer: C: Whats the point of genotype pruning before imputation?
... They are not pruning before imputation, pruning is a step before doing other QC steps, to calculate IBD and remove related individuals, or calculate PCs to remove outlier individuals based on ethnicity. As the final step of QC, there will be plink command something like: plink --bfile origina ...
written 3 days ago by zx87547.8k
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Comment: C: Whats the point of genotype pruning before imputation?
... Could you provide a link to that protocl: > standard to remove all SNPs in LD before imputation ...
written 4 days ago by zx87547.8k
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Comment: C: How separate one column in two columns?
... Related StackOverflow posts: - [Splitting a dataframe string column into multiple different columns](https://stackoverflow.com/q/18641951/680068) - [Remove everything after space in string](https://stackoverflow.com/q/9319242/680068) ...
written 5 days ago by zx87547.8k
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Answer: A: How to find pattern matching over range of columns but not present in other colu
... Using *data.table*, reshape wide-to-long, then get number of 1s and number of rows per "POS, pop", if numbers equal then subset. library(data.table) dt1 <- fread(" POS pop1 pop1 pop1 pop1 pop1 pop2 pop2 pop2 pop2 pop2 pop3 pop3 pop3 pop3 pop3 pop4 pop4 pop4 pop4 pop4 74 ...
written 12 days ago by zx87547.8k
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Comment: C: How to calculate overlap of peptides between different categories to create Ven
... Yes, as the your columns overlap fully TRUE/FALSE is not working, replace TRUE/FALSE with 1/0 in dcast, see below example: # example data df <-read.table(text = " T2 T3 QHDMGHMMR QHDMGHMMR RPGGEPSPEGTTGQSYNQYSQR RPGGEPSPEGTTGQSYNQYSQR KTDELPQLVTLPHPNLHGPEILDVPSTVQK K ...
written 17 days ago by zx87547.8k
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Comment: C: How to calculate overlap of peptides between different categories to create Ven
... You need to share your example CSV: `FN1.csv`, so that we can reproduce the problem. ...
written 17 days ago by zx87547.8k
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Answer: A: Error in strsplit(TCGABarcode, split = "-") : non-character argument
... We are passing some factors to `strsplit`, to reproduce: strsplit("my-factor-text", split = "-") # [[1]] # [1] "my" "factor" "text" strsplit(factor("my-factor-text"), split = "-") # Error in strsplit(factor("my-factor-text"), split = "-") : # non-character argum ...
written 17 days ago by zx87547.8k
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Answer: A: How to calculate overlap of peptides between different categories to create Ven
... Convert to TRUE/FALSE, then use limma venn counts: # example data df <-data.frame( TGEClass.known = c( "GVVEVTHDLQK", "LFYADHPFIFLVR", "SALQSINEWAAQTTDGK", "AVLSAEQLRDEEVHAGLGELLR" ), TGEClass.uknown = c( "GVVEVTHDLQK", "L ...
written 18 days ago by zx87547.8k
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Answer: A: Breaking PLINK.bim .bed .fam files into chromosomes
... No need for scripts, simple loop should work, something like: for chr in {1..23}; do \ plink --bfile myPlink --chr $chr --out myPlink_${chr}; \ done ...
written 21 days ago by zx87547.8k

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