Tutorial for autosomal calculators

[Petalpusher]

Is it possible to run gedmatch kit numbers in calculators outside gedmatch?

No, you need the raw datas, gedmatch numbers are just numbers tied to people's genomes in their database.

error message after entering the following

standardize('f.txt', company='23andMe')

ERROR: could not find function "standardize"



Standardize.r is in the folder? What am I doing wrong? K11 folder is in C as instructed??

I don't know if it's your error but you should run source('standardize.r') first and getting a new prompt, then standardize('f.txt', company='23andMe')


While f.txt has to be replaced by the actual name of your genome like Dibran16022017.txt

[Proto-Shaman]

Is it possible to run gedmatch kit numbers in calculators outside gedmatch?

well, this thread actually does not exist

[DarkWater]

does it work with raw data from Ancestry?

[Yinwang888]

Very nice explanation, thank you very much!

[Carlito's Way]

im trying to do this for a new calculator and im getting really mad because I cant get it to work, I have followed all the steps and I get no damn results

[Taiguaitiaoghyrmmumin]

These calculators are boring. The only thjng Im still interested is about haplogroups for genetics

[Lemgrant]

+

How to make 3D PCA in RStudio and perform hierarchical k-means clustering
https://youtu.be/_lZ_EqV-cZw


Eurogenes K13 datasheet: https://drive.google.com/file/d/1cDv...fwoAHewJ6/view

Script:

Spoiler!

install.packages("randomcoloR")
install.packages("factoextra")
install.packages("rgl")
install.packages("rmarkdown", repos = "https://cran.revolutionanalytics.com")

data01 <- read.csv(file.choose(), row.names = 'Population')
pca <- princomp(data01[,1:13], cor=TRUE, scores=TRUE)
summary(pca)
library(rgl) #load the package
plot3d(pca$scores[,1:3], col="red", type="p")
text3d(pca$scores[,1:3],texts=rownames(data01),font=2)
grid3d('x')
grid3d('y')
grid3d('z')

text3d(pca$loadings[,1:3], texts=rownames(pca$loadings), col="red")
coords <- NULL
for (i in 1:nrow(pca$loadings)) {
  coords <- rbind(coords, rbind(c(0,0,0),pca$loadings[i,1:3]))
}
lines3d(coords, col="red", lwd=4)

library(factoextra) #load the package
cl <- hkmeans(data01[,1:13],130) #130 clusters
data01$cluster <- as.factor(cl$cluster)
library(randomcoloR) #load the package
palette <- distinctColorPalette(130) #130 colors
palette(palette)
plot3d(pca$scores[,1:3], col=data01$cluster, main="Hierarchical k-means clusters")
text3d(pca$scores[,1:3],texts=rownames(data01),font=2, col=data01$cluster)

observer3d(0, 0, 40) # x, y, z

__________________________________________

and

How to make custom oracle in RStudio (Gedmatch, G25...)

https://www.youtube.com/watch?v=cFpBinU5E18


Algorithm: https://docs.google.com/document/d/1...gAZMCzx8A/edit

[Lucas]

+

How to make 3D PCA in RStudio and perform hierarchical k-means clustering
https://youtu.be/_lZ_EqV-cZw


Eurogenes K13 datasheet: https://drive.google.com/file/d/1cDv...fwoAHewJ6/view

Script:

Spoiler!

install.packages("randomcoloR")
install.packages("factoextra")
install.packages("rgl")
install.packages("rmarkdown", repos = "https://cran.revolutionanalytics.com")

data01 <- read.csv(file.choose(), row.names = 'Population')
pca <- princomp(data01[,1:13], cor=TRUE, scores=TRUE)
summary(pca)
library(rgl) #load the package
plot3d(pca$scores[,1:3], col="red", type="p")
text3d(pca$scores[,1:3],texts=rownames(data01),font=2)
grid3d('x')
grid3d('y')
grid3d('z')

text3d(pca$loadings[,1:3], texts=rownames(pca$loadings), col="red")
coords <- NULL
for (i in 1:nrow(pca$loadings)) {
  coords <- rbind(coords, rbind(c(0,0,0),pca$loadings[i,1:3]))
}
lines3d(coords, col="red", lwd=4)

library(factoextra) #load the package
cl <- hkmeans(data01[,1:13],130) #130 clusters
data01$cluster <- as.factor(cl$cluster)
library(randomcoloR) #load the package
palette <- distinctColorPalette(130) #130 colors
palette(palette)
plot3d(pca$scores[,1:3], col=data01$cluster, main="Hierarchical k-means clusters")
text3d(pca$scores[,1:3],texts=rownames(data01),font=2, col=data01$cluster)

observer3d(0, 0, 40) # x, y, z

__________________________________________

and

How to make custom oracle in RStudio (Gedmatch, G25...)

https://www.youtube.com/watch?v=cFpBinU5E18


Algorithm: https://docs.google.com/document/d/1...gAZMCzx8A/edit

Did you know that MyTrueAncestry used your tutorial to make their 3d plot lol?

[Lemgrant]

Did you know that MyTrueAncestry used your tutorial to make their 3d plot lol?

They have 3d plots? I saw only 2d pca. I made this so that everyone could make a 3d pca, since RStudio is a free software.
https://www.rstudio.com/products/rstudio/download/

[Mayuk24]

+

How to make 3D PCA in RStudio and perform hierarchical k-means clustering
https://youtu.be/_lZ_EqV-cZw


Eurogenes K13 datasheet: https://drive.google.com/file/d/1cDv...fwoAHewJ6/view

Script:

Spoiler!

install.packages("randomcoloR")
install.packages("factoextra")
install.packages("rgl")
install.packages("rmarkdown", repos = "https://cran.revolutionanalytics.com")

data01 <- read.csv(file.choose(), row.names = 'Population')
pca <- princomp(data01[,1:13], cor=TRUE, scores=TRUE)
summary(pca)
library(rgl) #load the package
plot3d(pca$scores[,1:3], col="red", type="p")
text3d(pca$scores[,1:3],texts=rownames(data01),font=2)
grid3d('x')
grid3d('y')
grid3d('z')

text3d(pca$loadings[,1:3], texts=rownames(pca$loadings), col="red")
coords <- NULL
for (i in 1:nrow(pca$loadings)) {
  coords <- rbind(coords, rbind(c(0,0,0),pca$loadings[i,1:3]))
}
lines3d(coords, col="red", lwd=4)

library(factoextra) #load the package
cl <- hkmeans(data01[,1:13],130) #130 clusters
data01$cluster <- as.factor(cl$cluster)
library(randomcoloR) #load the package
palette <- distinctColorPalette(130) #130 colors
palette(palette)
plot3d(pca$scores[,1:3], col=data01$cluster, main="Hierarchical k-means clusters")
text3d(pca$scores[,1:3],texts=rownames(data01),font=2, col=data01$cluster)

observer3d(0, 0, 40) # x, y, z

__________________________________________

and

How to make custom oracle in RStudio (Gedmatch, G25...)

https://www.youtube.com/watch?v=cFpBinU5E18


Algorithm: https://docs.google.com/document/d/1...gAZMCzx8A/edit

thanks so much .... btw I like giordano bruno too c;

I never try R or any data analysis before.... I didn't have any project on mind ... until now ....

I'm autodidact but can you ask you about ... nmonte or how I can create my costume G25 from raw files ?

I mean I just need some inside about how to translate data into coordinates ... I saw in other post about normalize data...

I want to made coordinates of my chromosomes... where can I start to do so ? Dx