Load a bigSNP from backing files into R.

snp_attach(rdsfile)

Arguments

rdsfile

The path of the ".rds" which stores the bigSNP object.

Value

The bigSNP object.

Details

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.

Examples

(bedfile <- system.file("extdata", "example.bed", package = "bigsnpr"))
#> [1] "C:/Users/au639593/Documents/R/win-library/3.6/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 15 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\\RtmpcTfdg6\\filed8452dc6b74.bk" #> ..$ is_read_only: logi FALSE #> ..$ address :<externalptr> #> ..$ address_rw :<externalptr> #> ..$ bk : chr "C:\\Users\\au639593\\AppData\\Local\\Temp\\RtmpcTfdg6\\filed8452dc6b74.bk" #> ..$ rds : chr "C:\\Users\\au639593\\AppData\\Local\\Temp\\RtmpcTfdg6\\filed8452dc6b74.rds" #> ..$ is_saved : logi TRUE #> ..$ type_chr : chr "unsigned char" #> ..$ type_size : int 1 #> ..$ 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#envRefClass, show#FBM #> $ 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