User: paolo002

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paolo002160
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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 18 months ago by paolo002160 • updated 18 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 20 months ago by paolo002160
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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 20 months ago by paolo002160
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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 20 months ago by paolo002160 • updated 20 months ago by RamRS30k
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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 21 months ago by paolo002160
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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 21 months ago by paolo002160
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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 21 months ago by paolo002160
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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 21 months ago by paolo002160 • updated 21 months ago by zx87549.6k
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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 21 months ago by paolo002160
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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 21 months ago by paolo002160

Latest awards to paolo002

Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How to retrieve the genes associated to a VCF file?
Supporter 20 months ago, voted at least 25 times.
Scholar 20 months ago, created an answer that has been accepted. For A: Assigning SNPs to gene names based on genomic coordinates
Student 24 months ago, asked a question with at least 3 up-votes. For Subsetting large list of SNPs with R

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