Category » HelixTree

There were 23 articles found in this category:

1. Interpreting the Correlation/Interaction view
   From the HelixTree Manual: The Correlation Interaction View The figure aboveshows a matrix of the selected variables in the order they were sorted in the Multitree Model window. The numbers appearing in the black diagonal blocks represent the average proportion of observations described by the ...
2. Creating a .dsf of a subset of SNPs
   Creating a DSF containing only a subset of markers can be done rather easily if you have applied a marker map to your spreadsheet. Note: The types of subsets you can create depend on the information contained within your marker map. For instance, if your marker map only contains chromosome and ...
3. Tutorial: How to Visualize LogRs and Segments in HelixTree
   In various live webinars and on our website, we have shown images similar to the one below, plotting each marker for a given sample vs. its mean log2 ratio (LogRs) and displaying visually how CNAM (actually HelixTree in this case) made the split (denoted by vertical magenta lines). There is not ...
4. Creating Marker Map files from Illumina's BeadStudio
   Using Illumina’s BeadStudio software you can create a marker map containing the SNPs, Chromosome and Physical Position pertaining your particular dataset under study. To generate the marker map: 1. Select >Analysis >Reports >Report Wizard 2. On the window that pops up check Final Re ...
5. EIGENSTRAT in HelixTree
   The technique implemented in HelixTree to correct input data for population stratification by principal component analysis is based on the program EIGENSTRAT with a few enhancements. This technique was pioneered at the Broad Institute. The PCA correction technique is described in [Price 2006]. ...
6. Dominant and Recessive Genetic Association Tests and Cardinality
   When running genetic association tests (population data) under the dominant and recessive model, genotypes are recoded according to the specified model and then tested for association. Suppose that the SNP we are looking at has 2 alleles, A and B. In this process, we choose the allele to model b ...
7. Hardware Requirements
   When working with very large datasets, what hardware recommendations do you have? The general guidelines now are the more memory and the more cores you have the better. When working with Whole Genome Datasets, a minimum of 2 GB of RAM is recommended. For many of our analyses such as PBAT and C ...
8. How to merge (append) datasets and spreadsheets with uneven columns
   If you have two spreadsheets with a different number of columns and want to join them, there are some initial considerations. Within the spreadsheets, the overlapping columns must have the exact same names. This procedure is sometimes used in joining datasets that were genotyped on different c ...
9. Does the adjusted p-value (Ap) include as possible splits those that do not contain the minimum number of observations in the nodes, as required in the tree options?
   The short answer is no. For tree splits, the factors used in the adjusted p calculations were derived from simulations on random data from the appropriate distribution (binary or normal) where no constraint was placed on the minimum observations in the nodes. Thus, if you have a constraint on th ...
10. Hardy Weinberg Equilibrium (HWE) differences between HelixTree and PBAT
    1. There are two HWE columns in PBAT. The "main" HWE column is for patients only and the other for parents only. HelixTree calculates HWE for all samples (not including deactivated rows.) 2. PBAT uses 2 degrees of freedom and HelixTree only one for its HWE calculations.
11. Can HelixTree handle microsatellite genotypes (or multi-allelic markers)?
    Yes, HelixTree can handle markers that are multi-allelic. If you have a multi-allelic marker HelixTree will still recognize the column as genetic and you can perform LD, HWE, etc. You will not be able to test for association through the Case/Control Association window, but instead use Interactiv ...
12. How do I transfer my license key to another computer?
    To transfer your license to another computer, you need to first contact Golden Helix Support at support@goldenhelix.com to update your license information. Please provide your Customer ID and the operating system to which you are moving HelixTree. Our Support Team will contact you within 1 bus ...
13. I have a manual license key. How do I get updates?
    You should be contacted by our Support Team with update instructions at each release. If you did not receive update instructions with the last release or need to receive them again, please contact support@goldenhelix.com or call us at (406) 585-8137.
14. How to reinstall HelixTree
    If you are reinstalling HelixTree on the same computer, you can use your existing license key. If you do not have your license key and/or would like the download link to latest version of the software, please contact support@goldenhelix.com. If you need to reinstall HelixTree on another comput ...
15. Access the Latest HelixTree Manual
    The latest HelixTree manual can be found in the folder where HelixTree.exe is stored on your computer. You must update HelixTree to the most recent version in order to have the most recent manual available. The HelixTree manual is also available here on the Golden Helix website.
16. Is there a recommended cutoff for Hardy Weinberg Equilibrium and minor allele frequency for whole genome analysis?
    We are really not sure if there are accepted rules of thumb, so a more cautious answer is, that it depends. There are certain population structures where large departures from HWE are legitimate, as well as regions of the genome prone to copy number deletions that could result in large departure ...
17. How does the random tree creation tool work in HelixTree?
    The random tree creation tool will build random tree models of your data, where the split variables are randomly chosen from a list of significant effects (by default 10 or less). These random trees can then be analyzed in various ways. We can look and see which variables are used across all the ...
18. The meaning of recursive split in HelixTree
    The recursive split will build a dendrogram or tree-like model. The top node is the root node and represents the entire data set. (n=number of observations, u=mean & s=standard deviation). From this root node other branches will grow, forming subgroups, and so on, until a termination criterion i ...
19. 2-Loci Genetic Plot, methodology, p-value computation
    The gist of the two-loci plot is that it is implemented as a categorical split using the underlying tree splitting methodology in HelixTree. Here is how the two-loci procedure works for each pair of markers: 1. Create categorical variables corresponding to the unique PAIRS of genotypes. This is ...
20. HelixTree seems to be missing menu items and/or icons for genetic features.
    Certain features such as Haplotype Frequency Estimation, Hardy Weinberg Equilibrium Plot, LD plot, etc. are only available when genetic data is in the spreadsheet. When you have genetic data in your spreadsheet and these features and corresponding buttons are missing, it usually means that genet ...