User: bastianxpfeifer

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40
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New User
Location:
Germany
Last seen:
1 year, 12 months ago
Joined:
2 years, 7 months ago
Email:
b**************@gmail.com

Posts by bastianxpfeifer

<prev • 12 results • page 1 of 2 • next >
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Answer: A: PopGenome software: error calculating neutrality_stats
... Thats weird, indeed. FAST=FALSE in the neutrality.stats() module does not fix the problem ? Ok, probably the following is a fast and dirty fix: GENOME.class_gla<-readVCF("chr8.vcf.gz",1000,"8",1,146364022,gffpath = "chr8.gff3") GENOME.class_gla <- set.outgroup(GENOME.class_gla, FALSE) gene ...
written 2.4 years ago by bastianxpfeifer40
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Comment: C: PopGenome software: error calculating neutrality_stats
... Thats weird, indeed. FAST=FALSE in the neutrality.stats() module does not fix the problem ? Ok, probably the following is a fast and dirty fix: GENOME.class_gla<-readVCF("chr8.vcf.gz",1000,"8",1,146364022,gffpath = "chr8.gff3") GENOME.class_gla <- set.outgroup(GENOME.class_gla, FALSE) gene ...
written 2.4 years ago by bastianxpfeifer40
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Answer: A: PopGenome software: error calculating neutrality_stats
... Hi, rm(list=ls()) gc() quit R (q()) and save the empty workspace. Note, you will delete all objects within your R session with these commands. Try again those PopGenome calls. I guess the error will disappear. Best, Bastian ...
written 2.4 years ago by bastianxpfeifer40
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Answer: A: Make fasta file from SNPs in two vcf files
... Whats about the R package PopGenome, readData(, format="VCF") region.as.fasta(...,type=1) Best, Bastian   ...
written 2.4 years ago by bastianxpfeifer40
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News: R package PopGenome: http://popgenome.weebly.com/
... A new website for the R-package PopGenome is available at http://popgenome.weebly.com/ ! This website will provide the newest PopGenome versions; source code and documentation files before they go on CRAN (which can take a while). I will also publish some NEWS regarding ongoing projects and new im ...
vcf R popgenome population genomics news written 2.5 years ago by bastianxpfeifer40
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Answer: A: PopGenome...ReadVCF. Cannot open the file. Why?
... Hi ALL, see also http://popgenome.weebly.com/ THX, all the best. Bastian ...
written 2.5 years ago by bastianxpfeifer40
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Answer: A: R, PopGenome Package. Cannot open file
... Hi ALL, see also http://popgenome.weebly.com/ THX, all the best. Bastian ...
written 2.5 years ago by bastianxpfeifer40
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Answer: A: PopGenome: How to read in multiple reference chromosomes.
... Hi ALL, see also http://popgenome.weebly.com/ THX, all the best. Bastian ...
written 2.5 years ago by bastianxpfeifer40
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Answer: A: PopGenome software: concatenating chromosomes and coalescent simulations
... Hi ALL, see also http://popgenome.weebly.com/ THX, all the best. Bastian ...
written 2.5 years ago by bastianxpfeifer40
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Comment: C: PopGenome software: concatenating chromosomes and coalescent simulations
... Hi, ok, seems you have SNP data in HapMap format and quite alot of unknown nucleotides like ./. try test <- readData("HapMapFolder", format="HapMap", include.unknown=TRUE) Note, PopGenome will take the position of the last SNP specified in the file to define the slot n.sites Best, B ...
written 2.6 years ago by bastianxpfeifer40

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Scholar 2.6 years ago, created an answer that has been accepted. For A: PopGenome: How to read in multiple reference chromosomes.

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