Need: A simple way to draw pedigrees. This R script will draw a PNG per family in a pedigree file.
Some answers here: https://twitter.com/brent_p/status/1222196118563381248 and others off-line:
Also see: https://twitter.com/Yutaka__Masuda/status/1222214145233182720
| *bcftools filter | |
| *Filter variants per region (in this example, print out only variants mapped to chr1 and chr2) | |
| qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz | |
| *printing out info for only 2 samples: | |
| bcftools view -s NA20818,NA20819 filename.vcf.gz | |
| *printing stats only for variants passing the filter: | |
| bcftools view -f PASS filename.vcf.gz |
| library(readxl) | |
| library(janitor) | |
| library(ggraph) | |
| library(igraph) | |
| df <- readxl::read_excel("/eurovision_song_contest_1975_2016.xlsx") %>% | |
| clean_names() | |
| df <- df[, c(5, 6, 1:4, 7)] |
| printname c.entry file line_no | |
| - do_arith R-4.0.3\src\main\arithmetic.c 411 | |
| ! do_logic R-4.0.3\src\main\logic.c 40 | |
| != do_relop R-4.0.3\src\main\relop.c 51 | |
| $ do_subset3 R-4.0.3\src\main\subset.c 1206 | |
| $<- do_subassign3 R-4.0.3\src\main\subassign.c 2081 | |
| %% do_arith R-4.0.3\src\main\arithmetic.c 411 | |
| %*% do_matprod R-4.0.3\src\main\array.c 1228 | |
| %/% do_arith R-4.0.3\src\main\arithmetic.c 411 | |
| & do_logic R-4.0.3\src\main\logic.c 40 |
| stratified <- function(df, group, size, select = NULL, | |
| replace = FALSE, bothSets = FALSE) { | |
| if (is.null(select)) { | |
| df <- df | |
| } else { | |
| if (is.null(names(select))) stop("'select' must be a named list") | |
| if (!all(names(select) %in% names(df))) | |
| stop("Please verify your 'select' argument") | |
| temp <- sapply(names(select), | |
| function(x) df[[x]] %in% select[[x]]) |
This is complete taken from Ryan D on biostar: http://www.biostars.org/p/2909/#16419
It takes a region in a format like "chr2:1234-3456". If an rs number is specified after the region, it will output the R^2 for every SNP in that region with the requested SNP; otherwise, it is all-vs-all.
| vif_func<-function(in_frame,thresh=10,trace=T,wts=NULL,...){ | |
| library(fmsb) | |
| if(any(!'data.frame' %in% class(in_frame))) in_frame<-data.frame(in_frame) | |
| if(is.null(wts)) | |
| wts <- rep(1, ncol(in_frame)) | |
| if(!is.null(wts)) | |
| if(length(wts)!=ncol(in_frame)) stop('length of weights must equal number of variables') |
