petrelharp local_pca issues

petrelharp / local_pca

Methods for examining PCA locally along the genome.

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issues

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summarize_run.Rmd cannot open file connection

#39 justanothervanessa closed 2 months ago
2
Add a simple and short example with public data

#38 petrelharp opened 2 months ago
0
better corners docs

#37 petrelharp closed 2 months ago
0
Add a manual if possible

#36 GabrieleNocchi closed 2 months ago
10
Issue with my file? Lots of different errors

#35 lilymaya closed 6 months ago
3
Error generating PCs of corners

#34 jkreinz closed 6 months ago
7
Error in cmdscale(pc.distmat[!na.inds, !na.inds], k = opt$nmds) : NA values not allowed in 'd'

#33 ltalignani closed 11 months ago
1
Error when I try to plot MDS

#32 ltalignani closed 11 months ago
3
run_lostruct.R error

#31 RCLynch414 closed 1 year ago
3
SNP filtering recommendations

#30 sjfleck closed 11 months ago
2
Error in `colnames<-`(`*tmp*`, value = out.colnames)

#29 Lin-Yuying closed 1 year ago
4
error in reading VCF

#28 ylevmirom closed 2 years ago
3
chromosome names gives me problems

#27 siv-n closed 2 years ago
4
github repo not installing with devtools

#26 josieparis closed 3 years ago
2
Displaying results error

#25 sjfleck closed 3 years ago
14
Fixtests

#24 petrelharp closed 3 years ago
0
Further fixes for tests etc

#23 kdm9 closed 3 years ago
4
Test that sample names with pipes don't break bcftools

#22 kdm9 closed 3 years ago
1
quote region string when using bcftools

#21 petrelharp closed 3 years ago
0
Issues with | in contig names

#20 kdm9 closed 3 years ago
7
The effect of sample number and relationship on local PCA results

#19 Axolotl233 closed 3 years ago
1
Questions regarding bcftools

#18 HanXiaoEvo closed 3 years ago
4
don't escape backslashes in bcftools calls

#17 petrelharp closed 4 years ago
3
Is vcf_windower compatible with the last versions of bcftools?

#16 clairemerot closed 4 years ago
15
allow many chroms per bcf

#15 petrelharp closed 4 years ago
3
Medicago example out of date

#14 sandyplus opened 4 years ago
1
Unable to plot PCs of the corners

#13 jguhlin closed 4 years ago
20
error when running on multiple scaffolds

#12 mariels closed 4 years ago
8
NA values in PCA and MDS results

#11 jdmanthey closed 4 years ago
5
error on the read in

#10 jkreinz closed 4 years ago
2
Error in computing distances

#9 zfuller5280 closed 5 years ago
5
Using lostruct package on pca data coming from other programs

#8 clairemerot closed 5 years ago
3
cmdscale issue

#7 owensgl closed 6 years ago
21
document medicago methods

#6 petrelharp closed 5 years ago
1
re-run medicago with distance instead of distance^2

#5 petrelharp closed 5 years ago
1
add sqrt to pc_dist

#4 petrelharp closed 7 years ago
1
improve documentation for win.fn in vcf_windower

#3 petrelharp closed 7 years ago
1
detect when data are not ACGT and give warning suggesting 'recode=FALSE'

#2 petrelharp closed 7 years ago
1
Update README.md

#1 cc2qe closed 7 years ago
1