library(vcfR)## Warning: package 'vcfR' was built under R version 4.2.2##
## ***** *** vcfR *** *****
## This is vcfR 1.13.0
## browseVignettes('vcfR') # Documentation
## citation('vcfR') # Citation
## ***** ***** ***** *****library(vegan)## Loading required package: permute## Loading required package: lattice## This is vegan 2.6-4library(ggplot2)
library(ggpubr)getwd()## [1] "C:/Users/Alexp/Documents/comp bio/Final Project"list.files(pattern="vcf")## [1] "my_snps.vcf.gz" "vcf_num.csv" "vcf_num_df.csv" "vcf_num_df2.csv"Set Up Data for R
my_vcf<-"my_snps.vcf.gz"
vcf<-vcfR::read.vcfR(my_vcf,convertNA = T)## Scanning file to determine attributes.
## File attributes:
## meta lines: 130
## header_line: 131
## variant count: 7591
## column count: 2513
##
Meta line 130 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 7591
## Character matrix gt cols: 2513
## skip: 0
## nrows: 7591
## row_num: 0
##
Processed variant 1000
Processed variant 2000
Processed variant 3000
Processed variant 4000
Processed variant 5000
Processed variant 6000
Processed variant 7000
Processed variant: 7591
## All variants processedvcf_num<-vcfR::extract.gt(vcf,
element="GT",
IDtoRowNames=F,
as.numeric=T,
convertNA=T)write.csv(vcf_num,file="vcf_num.csv",row.names = F)
list.files()## [1] "1000genomes_people_info2-1.csv" "data_preparation.html"
## [3] "data_preparation.Rmd" "Final Project.Rproj"
## [5] "final_report.html" "final_report.Rmd"
## [7] "my_data.csv" "my_snps.vcf.gz"
## [9] "rsconnect" "vcf_num.csv"
## [11] "vcf_num_df.csv" "vcf_num_df2.csv"vcf_num_t<-t(vcf_num)
vcf_num_df<-data.frame(vcf_num_t)
sample<-row.names(vcf_num_df)
vcf_num_df<-data.frame(sample,vcf_num_df)getwd()## [1] "C:/Users/Alexp/Documents/comp bio/Final Project"write.csv(vcf_num_df,file="vcf_num_df.csv",row.names = F)
list.files()## [1] "1000genomes_people_info2-1.csv" "data_preparation.html"
## [3] "data_preparation.Rmd" "Final Project.Rproj"
## [5] "final_report.html" "final_report.Rmd"
## [7] "my_data.csv" "my_snps.vcf.gz"
## [9] "rsconnect" "vcf_num.csv"
## [11] "vcf_num_df.csv" "vcf_num_df2.csv"Cleaning the Data
pop_meta<-read.csv(file="1000genomes_people_info2-1.csv")names(pop_meta)## [1] "pop" "super_pop" "sample" "sex" "lat" "lng"names(vcf_num_df)[1:10]## [1] "sample" "X1" "X2" "X3" "X4" "X5" "X6" "X7"
## [9] "X8" "X9"vcf_num_df2 <- merge(pop_meta,vcf_num_df,by="sample")
nrow(vcf_num_df)==nrow(vcf_num_df2)## [1] TRUEnames(vcf_num_df2)[1:15]## [1] "sample" "pop" "super_pop" "sex" "lat" "lng"
## [7] "X1" "X2" "X3" "X4" "X5" "X6"
## [13] "X7" "X8" "X9"getwd()## [1] "C:/Users/Alexp/Documents/comp bio/Final Project"write.csv(vcf_num_df2,file="vcf_num_df2.csv",row.names = F)
list.files()## [1] "1000genomes_people_info2-1.csv" "data_preparation.html"
## [3] "data_preparation.Rmd" "Final Project.Rproj"
## [5] "final_report.html" "final_report.Rmd"
## [7] "my_data.csv" "my_snps.vcf.gz"
## [9] "rsconnect" "vcf_num.csv"
## [11] "vcf_num_df.csv" "vcf_num_df2.csv"Omit Invariant Features
invar_omit <- function(x){
cat("Dataframe of dim",dim(x),"processed...\n")
sds <- apply(x,2,sd,na.rm=TRUE)
i_var0<-which(sds==0)
cat(length(i_var0),"columns removed\n")
if(length(i_var0)>0){
x<-x[,-i_var0]
}
return(x)
}names(vcf_num_df2)[1:10]## [1] "sample" "pop" "super_pop" "sex" "lat" "lng"
## [7] "X1" "X2" "X3" "X4"vcf_noinvar <-vcf_num_df2
vcf_noinvar <-invar_omit(vcf_noinvar[,-c(1:6)])## Dataframe of dim 2504 7591 processed...
## 1848 columns removedvcf_noinvar<-data.frame(vcf_num_df2[,c(1:6)],vcf_noinvar)
my_meta_N_invar_cols<-1848
dim(vcf_num_df2)## [1] 2504 7597dim(vcf_noinvar)## [1] 2504 5749head(vcf_noinvar)## sample pop super_pop sex lat lng X1 X2 X4 X5 X6 X7 X10 X11 X12
## 1 HG00096 GBR EUR male 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## 2 HG00097 GBR EUR female 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## 3 HG00099 GBR EUR female 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## 4 HG00100 GBR EUR female 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## 5 HG00101 GBR EUR male 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## 6 HG00102 GBR EUR female 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## X14 X15 X16 X17 X18 X19 X20 X21 X22 X23 X24 X25 X26 X27 X28 X29 X31 X33 X34
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## 4 0 0 0 0 1 0 0 0 0 0 0 0 0
## 5 0 0 0 0 1 0 0 0 0 0 0 0 0
## 6 0 0 0 1 1 0 0 0 0 0 0 0 0
## X1855 X1856 X1857 X1858 X1860 X1862 X1863 X1864 X1865 X1866 X1867 X1868 X1869
## 1 0 0 0 0 0 1 0 0 1 0 0 0 0
## 2 0 0 0 0 0 1 0 0 1 0 0 0 0
## 3 0 0 0 0 0 1 0 0 1 0 0 0 0
## 4 0 0 1 0 0 0 0 0 1 0 0 0 0
## 5 0 0 1 0 0 0 0 0 1 0 0 0 0
## 6 0 0 0 0 0 1 0 0 0 0 0 0 0
## X1870 X1871 X1872 X1873 X1874 X1875 X1876 X1878 X1879 X1881 X1882 X1883 X1884
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 1 0 0 0 0 1 0 0 0 0 1 0 0
## X1885 X1886 X1887 X1890 X1891 X1892 X1894 X1895 X1896 X1899 X1901 X1902 X1903
## 1 1 1 0 0 0 0 0 0 0 0 0 1 0
## 2 1 1 0 0 0 0 0 0 0 0 0 1 0
## 3 0 0 0 0 0 0 0 0 0 0 0 1 0
## 4 1 1 0 0 0 0 0 0 0 0 1 1 0
## 5 1 1 0 0 0 0 0 1 0 0 0 1 0
## 6 1 0 0 0 0 0 0 0 0 0 0 1 0
## X1904 X1905 X1907 X1908 X1909 X1910 X1911 X1912 X1913 X1915 X1916 X1917 X1919
## 1 0 0 0 0 0 0 0 0 0 0 0 0 1
## 2 0 0 0 0 0 0 0 0 0 0 0 0 1
## 3 0 0 0 0 0 0 0 0 0 0 0 0 1
## 4 0 0 0 0 0 0 0 0 0 0 0 0 1
## 5 0 0 0 0 1 0 0 0 1 0 0 0 1
## 6 0 0 0 0 0 0 0 0 0 1 0 0 1
## X1920 X1921 X1922 X1925 X1926 X1927 X1928 X1929 X1931 X1932 X1933 X1936 X1937
## 1 0 0 0 0 0 0 0 1 0 0 0 0 0
## 2 0 0 0 0 0 0 0 1 0 0 0 0 0
## 3 0 0 0 0 0 0 0 1 0 0 0 0 0
## 4 0 1 0 0 0 0 0 0 0 0 0 0 1
## 5 0 1 0 0 0 0 0 1 0 0 0 0 1
## 6 0 1 0 0 0 0 0 0 0 0 0 0 1
## X1940 X1941 X1942 X1944 X1945 X1946 X1947 X1948 X1951 X1952 X1954 X1955 X1956
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 1 0 0 1 0 0 0 0
## 5 0 0 0 0 0 1 0 0 0 0 0 0 0
## 6 0 0 0 0 0 2 1 0 0 0 0 0 0
## X1957 X1958 X1959 X1960 X1961 X1962 X1963 X1965 X1966 X1970 X1971 X1972 X1973
## 1 0 0 0 1 0 0 0 0 0 1 0 0 0
## 2 0 0 0 1 0 0 0 0 0 1 0 0 0
## 3 0 0 0 1 0 0 0 0 0 1 0 0 0
## 4 0 0 0 1 0 0 0 0 0 1 0 0 0
## 5 0 0 0 1 0 0 0 0 0 1 0 0 0
## 6 0 0 0 1 0 0 0 0 0 1 1 0 0
## X1974 X1975 X1976 X1977 X1978 X1979 X1980 X1981 X1982 X1983 X1984 X1985 X1986
## 1 0 0 0 2 0 0 0 0 0 0 0 0 0
## 2 0 0 0 2 0 0 0 0 0 0 0 0 0
## 3 0 0 0 2 0 0 0 0 0 0 0 0 0
## 4 0 0 0 3 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 1 0 0 0 0 0 0 1
## 6 0 0 0 1 0 0 0 0 0 0 0 0 0
## X1988 X1989 X1990 X1992 X1994 X1995 X1996 X1997 X1999 X2000 X2001 X2002 X2004
## 1 0 0 0 0 0 0 0 0 0 0 1 0 0
## 2 0 0 0 0 0 0 0 0 0 0 1 0 0
## 3 0 0 0 0 0 0 0 0 0 0 1 0 0
## 4 0 0 0 0 0 0 0 0 0 0 1 0 0
## 5 0 0 0 0 0 0 0 0 0 0 1 1 0
## 6 0 0 0 0 0 0 0 0 0 0 1 0 0
## X2006 X2007 X2008 X2009 X2010 X2011 X2012 X2013 X2015 X2016 X2017 X2018 X2020
## 1 0 0 0 0 0 0 0 0 0 0 1 0 0
## 2 0 0 0 0 0 0 0 0 0 0 1 0 0
## 3 0 0 0 0 0 0 0 0 0 0 1 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 1 0 0 0 0 0 0 0 0
## X2021 X2022 X2023 X2024 X2025 X2027 X2028 X2029 X2032 X2033 X2034 X2035 X2036
## 1 0 0 0 0 0 0 0 0 0 0 0 0 1
## 2 0 0 0 0 0 0 0 0 0 0 0 0 1
## 3 0 0 0 0 0 0 0 0 0 0 0 0 1
## 4 0 0 0 0 0 0 0 0 0 0 0 0 1
## 5 0 0 0 0 1 0 0 0 0 0 0 0 1
## 6 0 0 0 0 1 0 0 1 1 0 1 0 1
## X2037 X2040 X2041 X2042 X2043 X2045 X2046 X2047 X2048 X2050 X2052 X2053 X2054
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 1 0 0 0 0 0 0 0 0 1 0
## X2055 X2056 X2057 X2059 X2061 X2062 X2065 X2069 X2070 X2073 X2074 X2075 X2076
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 1 0 0 0 0 0 0 0 0 1 0 1
## 6 0 0 0 0 0 0 0 0 0 0 0 0 1
## X2078 X2080 X2083 X2084 X2085 X2086 X2087 X2088 X2090 X2091 X2092 X2095 X2096
## 1 0 0 0 0 0 0 0 0 0 0 0 0 1
## 2 0 0 0 0 0 0 0 0 0 0 0 0 1
## 3 0 0 0 0 0 0 0 0 0 0 0 0 1
## 4 0 0 0 0 0 0 0 0 1 0 0 0 1
## 5 0 0 1 0 0 0 1 0 0 0 0 0 0
## 6 0 0 1 0 0 1 0 0 0 1 0 0 0
## X2097 X2098 X2099 X2100 X2101 X2102 X2103 X2104 X2105 X2106 X2107 X2108 X2109
## 1 1 0 0 0 0 0 0 0 0 0 0 0 0
## 2 1 0 0 0 0 0 0 0 0 0 0 0 0
## 3 1 0 0 0 0 0 0 0 0 0 0 0 0
## 4 1 0 0 0 0 0 0 0 0 0 0 0 0
## 5 1 0 0 0 0 0 0 0 0 0 0 0 0
## 6 1 1 0 0 0 0 0 0 0 0 0 0 0
## X2110 X2111 X2112 X2113 X2114 X2115 X2119 X2120 X2122 X2123 X2124 X2128 X2130
## 1 0 0 0 0 0 0 0 0 1 0 1 0 0
## 2 0 0 0 0 0 0 0 0 1 0 1 0 0
## 3 0 0 0 0 0 0 0 0 1 0 0 1 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 1 0 0 1 0
## 6 0 0 0 0 0 0 0 0 1 0 1 0 0
## X2131 X2132 X2133 X2134 X2135 X2136 X2137 X2140 X2141 X2142 X2143 X2144 X2145
## 1 0 0 0 0 0 1 0 1 1 0 0 0 0
## 2 0 0 0 0 0 1 0 1 1 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 1 0 1 1 0 0 0 0
## X2146 X2147 X2148 X2149 X2152 X2153 X2155 X2157 X2159 X2160 X2162 X2163 X2164
## 1 0 0 0 0 0 0 0 1 0 0 0 0 0
## 2 0 0 0 0 0 0 0 1 0 0 0 0 0
## 3 0 0 0 0 0 0 0 1 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 1 0 0 0 0 0
## 6 0 0 0 0 0 0 0 1 0 0 0 0 0
## X2165 X2166 X2167 X2168 X2169 X2170 X2171 X2172 X2173 X2174 X2175 X2176 X2177
## 1 0 0 0 1 0 0 1 0 1 1 0 0 0
## 2 0 0 0 1 0 0 1 0 1 1 0 0 0
## 3 0 0 0 0 0 0 1 0 0 1 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 1 0 0 1 0 0 0
## 6 0 0 0 1 0 0 1 0 1 1 0 0 0
## X2178 X2180 X2185 X2187 X2188 X2190 X2191 X2192 X2193 X2194 X2196 X2197 X2198
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 1 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2199 X2201 X2202 X2205 X2206 X2207 X2208 X2209 X2210 X2211 X2212 X2213 X2214
## 1 0 0 0 0 0 0 0 0 1 0 0 0 0
## 2 0 0 0 0 0 0 0 0 1 0 0 0 0
## 3 0 0 0 0 1 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 1 0 0 0 0
## X2215 X2217 X2218 X2221 X2224 X2225 X2226 X2227 X2228 X2229 X2230 X2231 X2232
## 1 0 0 1 0 0 0 0 0 0 0 0 0 0
## 2 0 0 1 0 0 0 0 0 0 0 0 0 0
## 3 0 0 1 0 0 0 0 0 0 0 0 1 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 1 0 0 0 0 0 0 1 0
## 6 0 0 1 0 0 0 0 0 0 0 0 0 0
## X2235 X2236 X2237 X2240 X2242 X2243 X2246 X2247 X2250 X2253 X2254 X2255 X2256
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 1
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 1
## X2257 X2258 X2259 X2263 X2265 X2266 X2267 X2269 X2271 X2273 X2274 X2278 X2279
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 1 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2280 X2282 X2283 X2287 X2288 X2289 X2290 X2292 X2293 X2295 X2296 X2297 X2298
## 1 0 0 0 0 0 0 0 0 0 1 0 0 0
## 2 0 0 0 0 0 0 0 0 0 1 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 1 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 1 0 0 0 0 0 0 0 0 0 0 0 0
## X2299 X2300 X2302 X2303 X2304 X2306 X2307 X2308 X2309 X2310 X2312 X2313 X2314
## 1 0 0 0 0 0 0 1 1 0 0 0 0 0
## 2 0 0 0 0 0 0 1 1 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 1 1 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 1 0 0 0 0 0 0 0 0 0 0 0 0
## X2316 X2318 X2319 X2321 X2322 X2323 X2324 X2325 X2326 X2327 X2328 X2330 X2331
## 1 0 0 0 0 0 0 0 0 1 0 0 0 0
## 2 0 0 0 0 0 0 0 0 1 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 1 0 0 0 0 0 0 0 0 0 0 0 0
## X2332 X2334 X2335 X2336 X2337 X2340 X2342 X2343 X2344 X2345 X2346 X2347 X2351
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 1 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2352 X2353 X2354 X2355 X2356 X2358 X2359 X2360 X2361 X2362 X2363 X2366 X2368
## 1 0 0 0 0 0 2 0 0 0 0 0 0 0
## 2 0 0 0 0 0 2 0 0 0 0 0 0 0
## 3 0 0 0 0 0 2 0 0 0 0 0 1 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2370 X2372 X2373 X2374 X2375 X2376 X2377 X2378 X2380 X2381 X2382 X2383 X2384
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2385 X2389 X2391 X2392 X2393 X2394 X2396 X2397 X2398 X2399 X2401 X2402 X2403
## 1 0 0 0 0 0 0 0 0 0 0 0 1 0
## 2 0 0 0 0 0 0 0 0 0 0 0 1 0
## 3 0 0 0 0 0 0 0 0 0 0 0 1 0
## 4 0 0 0 0 0 0 0 0 0 0 0 1 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 1 0
## X2406 X2408 X2409 X2410 X2411 X2412 X2413 X2414 X2418 X2419 X2421 X2424 X2425
## 1 0 0 1 0 0 0 0 0 0 0 0 0 0
## 2 0 0 1 0 0 0 0 0 0 0 0 0 0
## 3 0 0 1 1 0 0 0 0 1 0 0 0 0
## 4 0 0 1 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 1 0 0 0 0 0 0 0 0 0 0
## X2427 X2428 X2429 X2430 X2431 X2432 X2434 X2435 X2437 X2440 X2441 X2444 X2446
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2449 X2450 X2452 X2453 X2454 X2455 X2456 X2458 X2459 X2461 X2463 X2465 X2466
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 1 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2467 X2470 X2475 X2476 X2477 X2478 X2479 X2481 X2482 X2484 X2485 X2487 X2488
## 1 0 0 0 0 0 0 0 1 0 0 0 0 0
## 2 0 0 0 0 0 0 0 1 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 1 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 1 0 0 0 0 0
## X2489 X2491 X2494 X2495 X2496 X2498 X2499 X2501 X2503 X2504 X2505 X2506 X2507
## 1 0 0 0 0 0 0 1 0 0 0 0 0 0
## 2 0 0 0 0 0 0 1 0 0 0 0 0 0
## 3 0 0 0 0 0 0 1 0 0 0 0 0 0
## 4 0 0 0 0 0 0 1 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 1 0 0 0 0 0 0
## X2509 X2510 X2512 X2513 X2514 X2516 X2517 X2518 X2519 X2520 X2521 X2522 X2523
## 1 0 0 1 0 0 1 0 0 0 1 0 0 0
## 2 0 0 1 0 0 1 0 0 0 1 0 0 0
## 3 0 0 0 1 0 1 0 0 0 0 1 0 0
## 4 0 0 0 0 0 1 0 0 0 1 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 1 0 0 0 1 0 0 0
## X2524 X2526 X2527 X2528 X2530 X2531 X2532 X2534 X2539 X2540 X2541 X2542 X2543
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2544 X2545 X2546 X2547 X2548 X2549 X2550 X2553 X2555 X2556 X2557 X2558 X2559
## 1 1 1 0 0 0 1 0 0 0 0 0 0 0
## 2 1 1 0 0 0 1 0 0 0 0 0 0 0
## 3 0 0 1 0 0 1 0 0 0 0 0 0 0
## 4 1 1 0 0 0 1 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 1 1 0 0 0 1 0 0 0 0 0 0 0
## X2560 X2561 X2562 X2563 X2564 X2565 X2566 X2567 X2568 X2572 X2573 X2574 X2575
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 1 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2576 X2579 X2580 X2582 X2583 X2584 X2585 X2586 X2587 X2588 X2589 X2590 X2593
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2595 X2596 X2597 X2598 X2599 X2600 X2601 X2602 X2603 X2604 X2605 X2606 X2607
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 1 0 1
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 1 0 0
## X2608 X2609 X2610 X2611 X2612 X2613 X2614 X2615 X2616 X2617 X2619 X2620 X2621
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 1 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2622 X2625 X2626 X2627 X2628 X2629 X2632 X2634 X2635 X2636 X2637 X2639 X2640
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 1 0 0 0 0 0 0 0 0 0 0
## X2641 X2646 X2647 X2648 X2650 X2651 X2652 X2653 X2654 X2655 X2656 X2658 X2659
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 1 0 1 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 1 0 0 0 0
## X2660 X2661 X2662 X2663 X2664 X2665 X2666 X2667 X2670 X2672 X2673 X2674 X2675
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 1 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 1 0
## X2676 X2678 X2679 X2680 X2682 X2683 X2684 X2685 X2687 X2688 X2689 X2690 X2691
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2692 X2693 X2694 X2696 X2697 X2699 X2702 X2704 X2706 X2707 X2710 X2711 X2712
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 1 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 1 0 0 0 0 0 0 0
## X2715 X2716 X2717 X2718 X2719 X2720 X2721 X2722 X2723 X2724 X2725 X2726 X2728
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 1 1 1 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 1 1 0 0 0 0 0 0 0
## X2729 X2730 X2731 X2732 X2733 X2734 X2735 X2736 X2737 X2738 X2740 X2742 X2743
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 1 1
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 1 1
## X2744 X2745 X2746 X2748 X2749 X2750 X2752 X2753 X2754 X2755 X2756 X2757 X2758
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 1 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 1 0 0 0 0
## X2759 X2760 X2761 X2762 X2763 X2766 X2767 X2768 X2769 X2770 X2771 X2772 X2773
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 1 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 1 0
## X2775 X2776 X2778 X2779 X2780 X2782 X2783 X2785 X2788 X2791 X2792 X2793 X2794
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 1 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 1 0 0 0 0
## X2795 X2796 X2799 X2800 X2801 X2802 X2803 X2804 X2806 X2807 X2808 X2809 X2810
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 1 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X2813 X2814 X2816 X2819 X2822 X2823 X2824 X2825 X2827 X2828 X2829 X2830 X2831
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 1 1 1 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 1 0 1 0 0 0 0 0
## X2832 X2833 X2835 X2836 X2838 X2839 X2840 X2841 X2842 X2843 X2845 X2846 X2848
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 1 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 1 0 0 0 0 0 0 0 0 0 0 0 0
## X2849 X2850 X2852 X2854 X2857 X2859 X2861 X2862 X2863 X2864 X2866 X2867 X2868
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X7362 X7363 X7364 X7365 X7367 X7368 X7369 X7370 X7371 X7372 X7374 X7375 X7376
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X7378 X7379 X7381 X7382 X7383 X7384 X7385 X7386 X7388 X7389 X7391 X7392 X7394
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
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## X7395 X7399 X7400 X7401 X7402 X7403 X7405 X7406 X7407 X7408 X7409 X7410 X7411
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X7497 X7500 X7501 X7502 X7503 X7504 X7505 X7506 X7507 X7509 X7511 X7513 X7514
## 1 0 0 0 0 0 0 1 0 0 1 0 0 0
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## X7515 X7516 X7517 X7519 X7520 X7521 X7525 X7526 X7527 X7528 X7530 X7531 X7532
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## 1 0 1 0 0 0 1 1 0 1 1 0 0 0
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## X7552 X7553 X7554 X7555 X7557 X7558 X7559 X7560 X7561 X7564 X7565 X7566 X7567
## 1 0 0 0 0 1 1 1 0 1 0 0 0 0
## 2 0 0 0 0 1 1 1 0 1 0 0 0 0
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## 6 0 0 0 0 1 1 1 0 1 0 0 0 0
## X7568 X7569 X7571 X7572 X7573 X7574 X7575 X7577 X7578 X7579 X7581 X7582 X7584
## 1 1 0 0 0 0 0 0 0 0 0 0 0 1
## 2 1 0 0 0 0 0 0 0 0 0 0 0 1
## 3 1 0 0 0 0 0 0 0 0 0 0 0 1
## 4 1 0 0 0 0 0 0 0 0 0 0 0 1
## 5 1 0 0 0 0 0 0 0 0 0 0 0 1
## 6 1 0 0 0 0 0 0 0 0 0 0 0 1
## X7585 X7586 X7587 X7588 X7589 X7590
## 1 0 0 1 0 0 0
## 2 0 0 1 0 0 0
## 3 0 0 1 0 0 0
## 4 0 0 1 0 0 0
## 5 0 0 1 0 0 0
## 6 0 0 1 0 0 0Remove Low-quality Data
find_NAs <-function(x){
NAs_TF <- is.na(x)
i_NA <- which(NAs_TF==TRUE)
N_NA<-(length(i_NA))
return (i_NA)
}N_rows <-nrow(vcf_noinvar)
N_NA <- rep(x=0,times=N_rows)
N_SNPs <- ncol(vcf_noinvar)
cat("This may take a minute")## This may take a minutefor(i in 1:N_rows){
i_NA<-find_NAs(vcf_noinvar[i,])
N_NA_i<-length(i_NA)
N_NA[i]<N_NA_i
}cutoff50 <-N_SNPs*.5
percent_NA <-N_NA/N_SNPs*100
any(percent_NA>50)## [1] FALSEmean(percent_NA)## [1] 0my_meta_N_meanNA_rows <-mean(percent_NA)
dim(vcf_noinvar)## [1] 2504 5749Imputation of NAs
mean_imputation <-function(df){
cat("This may take some time...")
n_cols <- ncol(df)
for(i in 1:n_cols){
column_i <-df[,i]
mean_i <-mean(column_i,na.rm=T)
NAs_i <- which(is.na(column_i))
N_NAs <- length(NAs_i)
column_i[NAs_i]<-mean_i
df[,i]<-column_i
}
return(df)
}names(vcf_noinvar)[1:10]## [1] "sample" "pop" "super_pop" "sex" "lat" "lng"
## [7] "X1" "X2" "X4" "X5"vcf_noNA <- vcf_noinvar
vcf_noNA[,-c(1:6)] <- mean_imputation(vcf_noinvar[,-c(1:6)])## This may take some time...Save data
write.csv(vcf_noNA,file="my_data.csv",row.names = F)