Moderator: zx8754

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zx87548.3k
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"If you torture the data long enough, it will confess." - Ronald Coase

Posts by zx8754

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Comment: C: filtering unique snps in vcf
... I think this is called "LD pruning". See related post, using *bcftools*: - https://www.biostars.org/p/338289/#339263 ...
written 13 hours ago by zx87548.3k
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Comment: C: Mapping common identifiers between two files
... Provide reproducible example input and expected output. Your code looks fine and should only return matching rows that have common `"ProbeID"`s in both files, test this example: merge(data.frame(x = 1:3, y = 11), data.frame(x = 2:4, z = 22), by = "x") # x y z # 1 2 11 22 ...
written 1 day ago by zx87548.3k
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Comment: C: How do i merge read counts and gene names of individual files into a single data
... Hello sambhav2mishra! We believe that this post does not fit the main topic of this site. Not related to bioinformatics. See related StackOverflow post: - [How to join (merge) data frames (inner, outer, left, right)](https://stackoverflow.com/q/1299871/680068) For this reason we have closed y ...
written 1 day ago by zx87548.3k
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Answer: C: trying to export DNA sequences into excel so that there are three nucleotides pe
... Please provide example input and expected output. Here is an example using **R**: x <- "12345678" n <- 3 substring(x, seq(1, nchar(x), n), seq(n, nchar(x) + n - 1, n)) # [1] "123" "456" "78" More solutions are at: - [Chopping a string into a vector of fixed width characte ...
written 5 days ago by zx87548.3k
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Answer: A: collapse rows of data frame by AGI transcript numbers to AGI gene number
... Clean up `target_id` column, then aggregate other multiple columns at once, see: # reproducible data df1 <- read.table(text = "target_id est_counts tpm AT1G01010.1 236 26.3 AT1G01020.2 55.0 12.2 AT1G01020.6 0 0 AT1G01020.1 25.2 4.8 AT1G01020.4 ...
written 7 days ago by zx87548.3k
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Comment: C: How to create a Venn Diagram from data frame and get the list of common Genes
... We could improve data preparation for `venn` as: input <- lapply(data[ -1 ], function(i) unique(data$Gene[ is.na(i) ])) ...
written 7 days ago by zx87548.3k
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Answer: A: Linux sort P-values with scientific notation
... Using both `g` and `n` at the same time gives an error: $ sort -gn input.txt sort: options '-gn' are incompatible Or: $ sort -k2ng,2 input.txt sort: options '-gn' are incompatible I am guessing, in your case it doesn't throw an error as we are using `g` for all columns and `n` for ...
written 8 days ago by zx87548.3k
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Comment: C: Error while running gatk
... Maybe edit your answer summarising the comments, then remove comments? ...
written 12 days ago by zx87548.3k
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Comment: C: select() not working in R
... Or use base subset: x <- mt_coding_variants[, "REF" ] ...
written 12 days ago by zx87548.3k
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Answer: A: Converting amino acid sequences to numerical values
... These examples should help you to get started: strsplit("XYZ", "") # [[1]] # [1] "X" "Y" "Z" lookup <- setNames(c(11, 22, 33), c("X", "Y", "Z")) lookup[ c("Z", "Z", "Y") ] # Z Z Y # 33 33 22 ...
written 12 days ago by zx87548.3k

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Scholar 4 months ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?
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Scholar 4 months ago, created an answer that has been accepted. For C: How to calculate r-squared with Haploview from different sources?

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