User: paolo002

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paolo002140
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Posts by paolo002

<prev • 37 results • page 1 of 4 • next >
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Set the root for a dendrogram
... Hi I have a data which is a binary matrix and I have generated a cluster dendrogram with the hclust function in R. First I normalise the values and then I plot. This is the code: mat.norm <- t(df / sqrt(2*rowSums(df))) plot(hclust(dist(mat.norm, "euclidean"))) My data consist of 9 colum ...
R written 4 months ago by paolo002140 • updated 4 months ago by Biostar ♦♦ 20
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Answer: A: How to retrieve the genes associated to a VCF file?
... Does you vcf file contain SNPs IDs in the form or rs numbers (ex: rs876643) and position? If so you should use the GenomicRanges package from Bioconductor to map the position of the SNPs to the location of the genes and retrieve the gene names. ...
written 5 months ago by paolo002140
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Comment: A: Phased Genotypes information
... Hi, thanks for your solutions to the problem, sorry the dots are there by mistake...so do not consider them, the rest is correct.thanks! ...
written 6 months ago by paolo002140
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Phased Genotypes information
... Hi all, first of all I apologise in case the following has been asked in previous posts but I am not able to find the solution to my problem. I have a data frame with a list of SNPs, their locations and the information of the Reference (REF) and Alternate (ALT) alleles. In addition I have informat ...
R linux written 6 months ago by paolo002140 • updated 6 months ago by RamRS22k
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Comment: C: Summarise statistics Fst values of SNPs list
... solved on stackoverflow: https://stackoverflow.com/questions/53874047/summarise-mean-median-data-frame-r ...
written 7 months ago by paolo002140
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Summarise statistics Fst values of SNPs list
... Hi, I have a data frame with Fst values for different SNPs windows. I would like to summarise the mean and median of the Fst values for each gene windows: gene chr start Nsites Fst01 Fst02 Fst12 1 AC002310.7 16 30591000 2 1 8. 5 ...
R written 7 months ago by paolo002140
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Comment: C: Subset top 5% values of data frames stored in list
... https://stackoverflow.com/questions/53724885/subset-multiple-data-frames-stored-inside-a-list in any case...this was the link but maybe there I did not explain my problem so well... ...
written 7 months ago by paolo002140
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Subset top 5% values of data frames stored in list
... Hi This is probably a question for stack overflow but I am posting it here because there I am not getting much replies, apologies for this. I have a 24 data frames with different number of rows and with various columns (for instance column SNPs ID and other columns with corresponding values for ea ...
R subset written 7 months ago by paolo002140 • updated 7 months ago by zx87547.8k
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Answer: A: calculating allele frequency difference or Fst value ?
... Hi Seta Personally I would recommend ANGSD (http://www.popgen.dk/angsd/index.php/ANGSD). It can calculate Fst in a straightforward way. ...
written 7 months ago by paolo002140
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Answer: A: Assigning SNPs to gene names based on genomic coordinates
... Hi, I have found a nice solution for doing that in R, I post it so maybe it might be useful to other people: Let' say you have a data frame (df) with list of SNPs ID (rs IDs and not annotated IDs) with chromosome number and location in Base Pairs (BP) on the genome ( I show the first 10 rows but th ...
written 7 months ago by paolo002140

Latest awards to paolo002

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to retrieve the genes associated to a VCF file?
Supporter 6 months ago, voted at least 25 times.
Scholar 6 months ago, created an answer that has been accepted. For A: Assigning SNPs to gene names based on genomic coordinates
Student 10 months ago, asked a question with at least 3 up-votes. For Subsetting large list of SNPs with R

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