Save a bigSNP after having made some modifications to it.
As bigSNP is an S3 class, you can add any slot you want
to an object of this class, then use snp_save to
save these modifications in the corresponding ".rds" backing file.
snp_save(x, version = NULL)A bigSNP.
the workspace format version to use. NULL
specifies the current default version (3). The only other supported
value is 2, the default from R 1.4.0 to R 3.5.0.
The (saved) bigSNP.
set.seed(1)
# Reading example
test <- snp_attachExtdata()
# I can add whatever I want to an S3 class
test$map$`p-values` <- runif(nrow(test$map))
str(test$map)
#> 'data.frame': 4542 obs. of 7 variables:
#> $ chromosome : int 1 1 1 1 1 1 1 1 1 1 ...
#> $ marker.ID : chr "SNP0" "SNP1" "SNP2" "SNP3" ...
#> $ genetic.dist: int 0 0 0 0 0 0 0 0 0 0 ...
#> $ physical.pos: int 112 1098 2089 3107 4091 5091 6107 7103 8090 9074 ...
#> $ allele1 : chr "A" "T" "T" "T" ...
#> $ allele2 : chr "T" "A" "A" "A" ...
#> $ p-values : num 0.266 0.372 0.573 0.908 0.202 ...
# Reading again
rds <- test$genotypes$rds
test2 <- snp_attach(rds)
str(test2$map) # new slot wasn't saved
#> 'data.frame': 4542 obs. of 6 variables:
#> $ chromosome : int 1 1 1 1 1 1 1 1 1 1 ...
#> $ marker.ID : chr "SNP0" "SNP1" "SNP2" "SNP3" ...
#> $ genetic.dist: int 0 0 0 0 0 0 0 0 0 0 ...
#> $ physical.pos: int 112 1098 2089 3107 4091 5091 6107 7103 8090 9074 ...
#> $ allele1 : chr "A" "T" "T" "T" ...
#> $ allele2 : chr "T" "A" "A" "A" ...
# Save it
snp_save(test)
# Reading again
test3 <- snp_attach(rds)
str(test3$map) # it is saved now
#> 'data.frame': 4542 obs. of 7 variables:
#> $ chromosome : int 1 1 1 1 1 1 1 1 1 1 ...
#> $ marker.ID : chr "SNP0" "SNP1" "SNP2" "SNP3" ...
#> $ genetic.dist: int 0 0 0 0 0 0 0 0 0 0 ...
#> $ physical.pos: int 112 1098 2089 3107 4091 5091 6107 7103 8090 9074 ...
#> $ allele1 : chr "A" "T" "T" "T" ...
#> $ allele2 : chr "T" "A" "A" "A" ...
#> $ p-values : num 0.266 0.372 0.573 0.908 0.202 ...
# The complicated code of this function
snp_save
#> function (x, version = NULL)
#> {
#> saveRDS(x, file = x$genotypes$rds, version = version)
#> invisible(x)
#> }
#> <bytecode: 0x000001b469dcd9c0>
#> <environment: namespace:bigsnpr>