Accessing and Replacing Parts of 'Mefa' Objects

Methods to access and replace parts (elements, slots) of "Mefa" objects.

Usage

xtab(x)
`xtab<-`(x, value)

samp(x)
`samp<-`(x, value)

taxa(x)
`taxa<-`(x, value)

Arguments

x

an object of S4 class "Mefa".

value

replacement value.

Details

The [ method ensures that the xtab sparse matrix part and the corresponding attribute tables are subsetted correctly.

Validity check is performed when replacing slots of an object.

Value

An object of S4 class "Mefa".

Author

Peter Solymos <solymos@ualberta.ca>

See also

Mefa

Examples

x <- data.frame(
    sample = paste("Sample", c(1,1,2,2,3,4), sep="."),
    species = c(paste("Species", c(1,1,1,2,3), sep="."),  "zero.pseudo"),
    count = c(1,2,10,3,4,0),
    stringsAsFactors = TRUE)
samp <- data.frame(samples=levels(x$sample), var1=1:2,
    stringsAsFactors = TRUE)
taxa <- data.frame(specnames=levels(x$species), var2=c("b","a"),
    stringsAsFactors = TRUE)
rownames(samp) <- samp$samples
rownames(taxa) <- taxa$specnames
x1 <- Xtab(count ~ sample + species, x)
x3 <- Mefa(x1, samp, taxa)

## accessing the xtab slot
xtab(x3)
#> 4 x 4 sparse Matrix of class "dgCMatrix"
#>          Species.1 Species.2 Species.3 zero.pseudo
#> Sample.1         3         .         .           .
#> Sample.2        10         3         .           .
#> Sample.3         .         .         4           .
#> Sample.4         .         .         .           .
## replacing the slot value
x1[3,1] <- 999
xtab(x3) <- x1
xtab(x3)
#> 4 x 4 sparse Matrix of class "dgCMatrix"
#>          Species.1 Species.2 Species.3 zero.pseudo
#> Sample.1         3         .         .           .
#> Sample.2        10         3         .           .
#> Sample.3       999         .         4           .
#> Sample.4         .         .         .           .

## accessing and replacing the samp slot
samp(x3)
#>           samples var1
#> Sample.1 Sample.1    1
#> Sample.2 Sample.2    2
#> Sample.3 Sample.3    1
#> Sample.4 Sample.4    2
samp(x3) <- NULL
samp(x3)
#> NULL
samp(x3) <- samp[1:3,]
samp(x3)
#>           samples var1
#> Sample.1 Sample.1    1
#> Sample.2 Sample.2    2
#> Sample.3 Sample.3    1
#> Sample.4     <NA>   NA

## accessing and replacing the taxa slot
taxa(x3)
#>               specnames var2
#> Species.1     Species.1    b
#> Species.2     Species.2    a
#> Species.3     Species.3    b
#> zero.pseudo zero.pseudo    a
taxa(x3) <- NULL
taxa(x3)
#> NULL
taxa(x3) <- taxa[1:3,]
taxa(x3)
#>             specnames var2
#> Species.1   Species.1    b
#> Species.2   Species.2    a
#> Species.3   Species.3    b
#> zero.pseudo      <NA> <NA>

## subsetting
unclass(x3[3:2, 1:2])
#> <S4 Type Object>
#> attr(,"xtab")
#> 2 x 2 sparse Matrix of class "dgCMatrix"
#>          Species.1 Species.2
#> Sample.3       999         .
#> Sample.2        10         3
#> attr(,"samp")
#>           samples var1
#> Sample.3 Sample.3    1
#> Sample.2 Sample.2    2
#> attr(,"taxa")
#>           specnames var2
#> Species.1 Species.1    b
#> Species.2 Species.2    a
#> attr(,"join")
#> [1] "left"
unclass(x3[3:2,])
#> <S4 Type Object>
#> attr(,"xtab")
#> 2 x 4 sparse Matrix of class "dgCMatrix"
#>          Species.1 Species.2 Species.3 zero.pseudo
#> Sample.3       999         .         4           .
#> Sample.2        10         3         .           .
#> attr(,"samp")
#>           samples var1
#> Sample.3 Sample.3    1
#> Sample.2 Sample.2    2
#> attr(,"taxa")
#>             specnames var2
#> Species.1   Species.1    b
#> Species.2   Species.2    a
#> Species.3   Species.3    b
#> zero.pseudo      <NA> <NA>
#> attr(,"join")
#> [1] "left"
unclass(x3[,1:2])
#> <S4 Type Object>
#> attr(,"xtab")
#> 4 x 2 sparse Matrix of class "dgCMatrix"
#>          Species.1 Species.2
#> Sample.1         3         .
#> Sample.2        10         3
#> Sample.3       999         .
#> Sample.4         .         .
#> attr(,"samp")
#>           samples var1
#> Sample.1 Sample.1    1
#> Sample.2 Sample.2    2
#> Sample.3 Sample.3    1
#> Sample.4     <NA>   NA
#> attr(,"taxa")
#>           specnames var2
#> Species.1 Species.1    b
#> Species.2 Species.2    a
#> attr(,"join")
#> [1] "left"