Load a bigSNP from backing files into R.
snp_attach(rdsfile)The path of the ".rds" which stores the bigSNP object.
The bigSNP object.
This is often just a call to readRDS. But it also checks if you have moved the two (".bk" and ".rds") backing files to another directory.
(bedfile <- system.file("extdata", "example.bed", package = "bigsnpr"))
#> [1] "C:/Users/au639593/AppData/Local/Temp/RtmpCcuoXf/temp_libpath50e85e914cf4/bigsnpr/extdata/example.bed"
# Reading the bedfile and storing the data in temporary directory
rds <- snp_readBed(bedfile, backingfile = tempfile())
# Loading the data from backing files
test <- snp_attach(rds)
str(test)
#> List of 3
#> $ genotypes:Reference class 'FBM.code256' [package "bigstatsr"] with 16 fields
#> ..$ extptr :<externalptr>
#> ..$ extptr_rw :<externalptr>
#> ..$ nrow : int 517
#> ..$ ncol : int 4542
#> ..$ type : Named int 1
#> .. ..- attr(*, "names")= chr "unsigned char"
#> ..$ backingfile : chr "C:\\Users\\au639593\\AppData\\Local\\Temp\\RtmpITJXCm\\file5f8c1312c29.bk"
#> ..$ is_read_only: logi FALSE
#> ..$ address :<externalptr>
#> ..$ address_rw :<externalptr>
#> ..$ bk : chr "C:\\Users\\au639593\\AppData\\Local\\Temp\\RtmpITJXCm\\file5f8c1312c29.bk"
#> ..$ rds : chr "C:\\Users\\au639593\\AppData\\Local\\Temp\\RtmpITJXCm\\file5f8c1312c29.rds"
#> ..$ is_saved : logi TRUE
#> ..$ type_chr : chr "unsigned char"
#> ..$ type_size : int 1
#> ..$ file_size : num 2348214
#> ..$ code256 : num [1:256] 0 1 2 NA NA NA NA NA NA NA ...
#> ..and 26 methods, of which 12 are possibly relevant:
#> .. add_columns, as.FBM, bm, bm.desc, check_dimensions,
#> .. check_write_permissions, copy#envRefClass, initialize, initialize#FBM,
#> .. save, show#FBM, show#envRefClass
#> $ fam :'data.frame': 517 obs. of 6 variables:
#> ..$ family.ID : chr [1:517] "POP1" "POP1" "POP1" "POP1" ...
#> ..$ sample.ID : chr [1:517] "IND0" "IND1" "IND2" "IND3" ...
#> ..$ paternal.ID: int [1:517] 0 0 0 0 0 0 0 0 0 0 ...
#> ..$ maternal.ID: int [1:517] 0 0 0 0 0 0 0 0 0 0 ...
#> ..$ sex : int [1:517] 0 0 0 0 0 0 0 0 0 0 ...
#> ..$ affection : int [1:517] 1 1 2 1 1 1 1 1 1 1 ...
#> $ map :'data.frame': 4542 obs. of 6 variables:
#> ..$ chromosome : int [1:4542] 1 1 1 1 1 1 1 1 1 1 ...
#> ..$ marker.ID : chr [1:4542] "SNP0" "SNP1" "SNP2" "SNP3" ...
#> ..$ genetic.dist: int [1:4542] 0 0 0 0 0 0 0 0 0 0 ...
#> ..$ physical.pos: int [1:4542] 112 1098 2089 3107 4091 5091 6107 7103 8090 9074 ...
#> ..$ allele1 : chr [1:4542] "A" "T" "T" "T" ...
#> ..$ allele2 : chr [1:4542] "T" "A" "A" "A" ...
#> - attr(*, "class")= chr "bigSNP"
dim(G <- test$genotypes)
#> [1] 517 4542
G[1:8, 1:8]
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
#> [1,] 0 0 2 0 1 1 0 2
#> [2,] 1 0 1 0 0 1 0 2
#> [3,] 0 1 1 0 2 1 0 2
#> [4,] 0 0 2 0 2 1 0 2
#> [5,] 1 0 0 0 2 2 1 0
#> [6,] 0 1 0 0 2 1 0 0
#> [7,] 0 1 1 0 2 2 1 1
#> [8,] 1 0 1 1 1 1 0 1