Clump function r

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August undefined, 2024

Webapp Apply a function to all cells, across layers, typically to summarize (as in base::apply) tapp Apply a function to groups of layers (as in base::tapply and stats::aggregate) lapp Apply a function to using the layers of a SpatRaster as variables sapp Apply a function to each layer rapp Apply a function to a spatially variable range of layers WebGibran Hemani. Source: vignettes/guide.Rmd. The IEU GWAS database comprises over 10,000 curated, QC’d and harmonised complete GWAS summary datasets and can be queried using an API. See here for documentation on the API itself. This R package is a wrapper to make generic calls to the API, plus convenience functions for specific queries.

clump: Detect clumps in raster: Geographic Data Analysis and Modeling

WebJun 22, 2024 · This function interacts with the OpenGWAS API, which houses LD reference panels for the 5 super-populations in the 1000 genomes reference panel. It includes only … Webld_clump_api <- function ( dat, clump_kb=10000, clump_r2=0.1, clump_p, pop="EUR", access_token= check_access_token ()) { res <- api_query ( 'ld/clump', query = list ( rsid … rajeku unath

Clump and eliminate classes in a raster in ArcMap or R

WebFeb 11, 2012 · However, a value of 1 for clump thickness is different than a value of 1 for bare nuclei. Unless we label the value, we only have the frequencies of the numbers 1-10 in the matrix, without knowing what they correspond to. ... this code is different than the code that appeared on r-bloggers. That code has a function called create_corpus which ... Webclump: Regroup observational data into even clumps of individuals. Description This function provides a easy way to regroup recorded data into groups of same number of … WebFeb 4, 2024 · The R package gdistance provides classes and functions to calculate various distance measures and routes in heterogeneous geographic spaces represented as grids. Least-cost distances as well as more complex distances based on (constrained) random walks can be calculated. Also the corresponding routes or probabilities of … rajekwesi

terra-package : Description of the methods in the terra package

Webclump_kb. Clumping window, default is 10000. clump_r2. Clumping r2 cutoff. ... This function does put load on the OpenGWAS servers, which makes life more difficult for other users. We have implemented a method and made available the LD reference panels to perform clumping locally, see ieugwasr::ld_clump() and related vignettes for details. ... WebTwoSampleMR/R/ld.R. #' Uses PLINK clumping method, where SNPs in LD within a particular window will be pruned. The SNP with the lowest p-value is retained. #' This function interacts with the OpenGWAS API, which houses LD reference panels for the 5 super-populations in the 1000 genomes reference panel. It includes only bi-allelic SNPs … dr david jupina orthopedicWebSep 19, 2014 · Clump and eliminate classes in a raster in ArcMap or R. after interpolation of sediment classes, I obtained a raster which looks like the image below (sample of the … raje koothrappali

"Webclump function - RDocumentation 0.1.0 clump: Clump Description Groups cells that form physically discrete areas, assigning them unique identifiers. Usage clump (input, output, … " - Clump function r

Clump function r

Clump raster cells into patches, with optional neighbourhood …

WebIf they are not then #' some functions e.g. [`ld_clump`] will exclude them from the analysis, #' so you may want to consider how to handle those variants in your data. #' #' @param rsid Array of rsids to check #' @param pop Super-population to use as reference panel. Default = `"EUR"`. #' Options are `"EUR"`, `"SAS"`, `"EAS"`, `"AFR"`, `"AMR ... http://www.rtexttools.com/blog/classifying-cancer-as-benign-or-malignant-using-rtexttools

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WebDetails. The p-values provided through argument p are assumed to correspond to the result of an association test with the SNPs of x.. The aim of the function is to construct cluster of SNPs in strong LD with associated SNPs. The algorithm first seeks the SNP with the lowest p-value (below p.threshold) ; this SNP will be the 'index' of a cluster.The corresponding … WebThis function interacts with the OpenGWAS API, which houses LD reference panels for the 5 super-populations in the 1000 genomes reference panel. It includes only bi …

WebNov 13, 2024 · setDT(df) The difference between the two approaches is: data.table(df) function will create a copy of df and convert it to a data.table. Whereas, setDT(df) converts it to a data.table inplace. That means, the df itself gets converted to a data.table and you don’t have to assign it to a different object. WebThe function CluMP_proﬁles provides a description (proﬁle) for each cluster. The description is in the form of a summary list containing descriptive statistics of a cluster variable, time variable, cluster parameters and other variables (covariates), both continuous and categorical.

WebThis function returns the raster cell values for a RasterLayer or RasterBrick object that are currently in memory (typically after read* has been used). WebSource: vignettes/stars6.Rmd. Here’s an attempt at the table describing how raster functions map to stars functions, discussed in issue #122 . This table uses the functionality of the raster package as a template; it may be incomplete, imprecise or plain wrong, so take it with a pinch of salt. Any comment or correction is hugely appreciated ...

WebR Documentation Detect clumps Description Detect clumps (patches) of connected cells. Each clump gets a unique ID. NA and zero are used as background values (i.e. these …

Webr.clump finds all areas of contiguous cell category values (connected components) in the input raster map. NULL values in the input are ignored. It assigns a unique category … dr david jue napaWebclump_kb. Clumping window, default is 10000. clump_r2. Clumping r2 cutoff. ... This function does put load on the OpenGWAS servers, which makes life more difficult for … dr david kahana probioticsWebClumping. Here, we use an LD reference panel to identify SNPs that are in LD with the top signals from a GWAS. The algorithm sequentially chooses the top SNP, removes all SNPs in LD above some threshold within some window, then goes on to the next top hit and repeats the pruning process, until no more SNPs are left above the specified p-value ... dr david jurkovich cardiologyWebDeleting pixels of a certain class that are connected to less than 2 other cells in R? 1 QGIS 3.6.2 with GRASS - raster calculator - Raster1 + Raster2 returns missing pixels dr. david kanarek long grove ilWebR/clump.R defines the following functions: CluMP. CluMP: Cluster Micro-Panel (longitudinal) Data employing the CluMP... CluMP_profiles: Summary characteristics of identified clusters via CluMP CluMP_view: Cluster profiles' (CluMP results) visualisation GeneratePanel: Generate an artificial Micro-Panel (longitudinal) Data OptiNum: Finding … dr david jueWebThe function CluMP_proﬁles provides a description (proﬁle) for each cluster. The description is in the form of a summary list containing descriptive statistics of a cluster … rajek tom bradyWebGet list of studies with available GWAS summary statistics through API. Infer ancestry of GWAS dataset by matching against 1000 genomes allele frequencies. Wrapper for clump function using local plink binary and ld reference dataset. Perform fast phewas of a specific variants against all available GWAS datasets. rajek kladno