User: blacktomato27

gravatar for blacktomato27
Reputation:
20
Status:
New User
Location:
United States
Last seen:
3 months ago
Joined:
4 years, 11 months ago
Email:
b************@gmail.com

about me

Posts by blacktomato27

<prev • 30 results • page 1 of 3 • next >
0
votes
0
answers
189
views
0
answers
Comment: C: how to convert genetic distance matrix to dataframe and rank genotypes based on
... Dear H.Mon Thanks lot for your reply and i am sorry inconvenience caused because of file format. I added new csv file fomat please have look on it, first sheet contains data i have and results sheet is what i would like to get after running code, https://www.dropbox.com/s/wo4tawgvhob476v/New%20Micr ...
written 3 months ago by blacktomato2720
0
votes
0
answers
189
views
0
answers
how to convert genetic distance matrix to dataframe and rank genotypes based on distance?
... Hi to all I got genetic distance matrix based snp genotyping data of 10 individuals in matrix format and now I want convert it into data frame format like genotype1 in columnA and genotype 2 in column B and distance between them in column C and also rank them genotype wise for easy comparisons. Here ...
R snp written 3 months ago by blacktomato2720 • updated 3 months ago by h.mon16k
0
votes
0
answers
439
views
0
answers
(Closed) how to create lower or upper triangle distance matrix in R?
... Hi to all Good Afternoon I got data like this 1 2 3 4 5 A 0.1 0.2 0.3 0.5 0.6 B 0.7 0.8 0.9 1 1.1 C 1.2 1.3 1.4 1.5 1.6 D 1.7 1.8 1.9 2 2.1 E 2.2 2.3 2.4 2.5 2.6 and now I want to create lower triangle matrix like this 1 2 3 4 5 A B C D E 1 0 2 0.1 ...
R written 5 months ago by blacktomato2720 • updated 5 months ago by Michael Dondrup44k
0
votes
0
answers
251
views
0
answers
Comment: C: how to select set of representative gentypes (corset) from group of genotypes?
... Dear Kevin Good Afternoon Thank you very much for your reply. Actually this power version was expired and not updated from last 10 years and i got his information at this (https://brcwebportal.cos.ncsu.edu/powermarker/). Coreset means for example if i want to sequence let say 100 genotypes (genoty ...
written 6 months ago by blacktomato2720
0
votes
0
answers
251
views
0
answers
how to select set of representative gentypes (corset) from group of genotypes?
... Hi to all Good Afternoon I have genotyping data (SNPs) of 200 plants and I want to select best representative lines corset (let say 50) from these 200 lines based SNP genotyping data. Previously I did it in power marker software but now it is not working anymore. I would like to know is there any o ...
R snp written 6 months ago by blacktomato2720
0
votes
0
answers
260
views
0
answers
how to make groups or strucuration of individuals in R?
... Hi to all Good Morning I have 93 individuals with 395 SNPs genotype data with me and there is no population information available for those individuals. Now I would like group those individuals into certain groups based on their genetic similarity but not like dendrogram. I checked DAPC function in ...
R written 8 months ago by blacktomato2720
0
votes
0
answers
267
views
0
answers
why pvclust is not identifying significant clusters?
... Dear all good evening i am making bootstrap dendrogram in R and goal is to identify siginificant clusters out of tree with PVCLUST package. I am getting only two major clusters and not getting significant subclusters eventhough AU/BP values are greater than 95. can any one help me to find out where ...
R written 8 months ago by blacktomato2720
0
votes
0
answers
406
views
0
answers
How to calculate LD values of SNP based on chromosomal positions and their call rate?
... Hi to all Good Afternoon I have file containing SNPs (affy 44k chip) with their call rate and chromosomal positions with me and these belongs to rice crop. Now how can i calculate LD values (r2) for these SNPs, my basic objective is to select tag SNPs based on LD for genotyping work. any help with ...
R snp written 9 months ago by blacktomato2720
1
vote
2
answers
661
views
2
answers
Comment: C: how to make bootstrapped tree in PVCLUST package with SNP genotyping data?
... Dear Kevin thanks lot for your help and your code working perfectly Great help Regards ...
written 9 months ago by blacktomato2720
0
votes
2
answers
661
views
2
answers
Answer: A: how to make bootstrapped tree in PVCLUST package with SNP genotyping data?
... Dear Kevin Good Morning Thanks lot for your help and time spent on solving my problem. I formatted my data as you suggested like 0,1,2 but for some reason it is not working as expected, ok leave it I will go through PVCLUST package only. I would like to know how I can use your above function to run ...
written 9 months ago by blacktomato2720

Latest awards to blacktomato27

Popular Question 6 months ago, created a question with more than 1,000 views. For How to convert SNP genotyping excel file to .MEGA file format
Scholar 9 months ago, created an answer that has been accepted. For A: how to compare 1st row and 1st column value with rest of the row values in R?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Snp Selection For Genotyping
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Perl Script To Select Snp Assays
Popular Question 3.9 years ago, created a question with more than 1,000 views. For how to make separate scatter graphs for separate groups with same format in R?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 568 users visited in the last hour