S4Vectors (version 0.10.2)

DataFrame-class: DataFrame objects

Description

The DataFrame class extends the DataTable virtual class and supports the storage of any type of object (with length and [ methods) as columns.

Constructor

: Constructs a DataFrame in similar fashion to data.frame. Each argument in ... is coerced to a DataFrame and combined column-wise. No special effort is expended to automatically determine the row names from the arguments. The row names should be given in row.names; otherwise, there are no row names. This is by design, as row names are normally undesirable when data is large. If check.names is TRUE, the column names will be checked for syntactic validity and made unique, if necessary. To store an object of a class that does not support coercion to DataFrame, wrap it in I(). The class must still have methods for length and [.

Accessors

In the following code snippets, x is a DataFrame.

dim(x): Get the length two integer vector indicating in the first and second element the number of rows and columns, respectively.

dimnames(x), dimnames(x) <- value: Get and set the two element list containing the row names (character vector of length nrow(x) or NULL) and the column names (character vector of length ncol(x)).

Coercion

as(from, "DataFrame"): By default, constructs a new DataFrame with from as its only column. If from is a matrix or data.frame, all of its columns become columns in the new DataFrame. If from is a list, each element becomes a column, recycling as necessary. Note that for the DataFrame to behave correctly, each column object must support element-wise subsetting via the [ method and return the number of elements with length. It is recommended to use the DataFrame constructor, rather than this interface.

as.list(x): Coerces x, a DataFrame, to a list.

as.data.frame(x, row.names=NULL, optional=FALSE): Coerces x, a DataFrame, to a data.frame. Each column is coerced to a data.frame and then column bound together. If row.names is NULL, they are retrieved from x, if it has any. Otherwise, they are inferred by the data.frame constructor. NOTE: conversion of x to a data.frame is not supported if x contains any list, SimpleList, or CompressedList columns.

as(from, "data.frame"): Coerces a DataFrame to a data.frame by calling as.data.frame(from).

as.matrix(x): Coerces the DataFrame to a matrix, if possible.

Subsetting

In the following code snippets, x is a DataFrame.

x[i,j,drop]: Behaves very similarly to the [.data.frame method, except i can be a logical Rle object and subsetting by matrix indices is not supported. Indices containing NA's are also not supported.

x[i,j] <- value: Behaves very similarly to the [<-.data.frame method.

x[[i]]: Behaves very similarly to the [[.data.frame method, except arguments j and exact are not supported. Column name matching is always exact. Subsetting by matrices is not supported.

x[[i]] <- value: Behaves very similarly to the [[<-.data.frame method, except argument j is not supported.

Combining

In the following code snippets, x is a DataFrame.

rbind(...): Creates a new DataFrame by combining the rows of the DataFrame objects in .... Very similar to rbind.data.frame, except in the handling of row names. If all elements have row names, they are concatenated and made unique. Otherwise, the result does not have row names. Currently, factors are not handled well (their levels are dropped). This is not a high priority until there is an XFactor class.

cbind(...): Creates a new DataFrame by combining the columns of the DataFrame objects in .... Very similar to cbind.data.frame, except row names, if any, are dropped. Consider the DataFrame as an alternative that allows one to specify row names.

Details

On the whole, the DataFrame behaves very similarly to data.frame, in terms of construction, subsetting, splitting, combining, etc. The most notable exception is that the row names are optional. This means calling rownames(x) will return NULL if there are no row names. Of course, it could return seq_len(nrow(x)), but returning NULL informs, for example, combination functions that no row names are desired (they are often a luxury when dealing with large data).

As DataFrame derives from Vector, it is possible to set an annotation string. Also, another DataFrame can hold metadata on the columns.

For a class to be supported as a column, it must have length and [ methods, where [ supports subsetting only by i and respects drop=FALSE. Optionally, a method may be defined for the showAsCell generic, which should return a vector of the same length as the subset of the column passed to it. This vector is then placed into a data.frame and converted to text with format. Thus, each element of the vector should be some simple, usually character, representation of the corresponding element in the column.

See Also

• DataTable and SimpleList which DataFrame extends directly.

Examples

score <- c(1L, 3L, NA)
counts <- c(10L, 2L, NA)
row.names <- c("one", "two", "three")
  
df <- DataFrame(score) # single column
df[["score"]]
df <- DataFrame(score, row.names = row.names) #with row names
rownames(df)
  
df <- DataFrame(vals = score) # explicit naming
df[["vals"]]

# arrays
ary <- array(1:4, c(2,1,2))
sw <- DataFrame(I(ary))  
  
# a data.frame
sw <- DataFrame(swiss)
as.data.frame(sw) # swiss, without row names
# now with row names
sw <- DataFrame(swiss, row.names = rownames(swiss))
as.data.frame(sw) # swiss

# subsetting
    
sw[] # identity subset
sw[,] # same

sw[NULL] # no columns
sw[,NULL] # no columns
sw[NULL,] # no rows

## select columns
sw[1:3]
sw[,1:3] # same as above
sw[,"Fertility"]
sw[,c(TRUE, FALSE, FALSE, FALSE, FALSE, FALSE)]

## select rows and columns
sw[4:5, 1:3]
  
sw[1] # one-column DataFrame
## the same
sw[, 1, drop = FALSE]
sw[, 1] # a (unnamed) vector
sw[[1]] # the same
sw[["Fertility"]]

sw[["Fert"]] # should return 'NULL'
 
sw[1,] # a one-row DataFrame
sw[1,, drop=TRUE] # a list

## duplicate row, unique row names are created
sw[c(1, 1:2),]

## indexing by row names  
sw["Courtelary",]
subsw <- sw[1:5,1:4]
subsw["C",] # partially matches

## row and column names
cn <- paste("X", seq_len(ncol(swiss)), sep = ".")
colnames(sw) <- cn
colnames(sw)
rn <- seq(nrow(sw))
rownames(sw) <- rn
rownames(sw)

## column replacement

df[["counts"]] <- counts
df[["counts"]]
df[[3]] <- score
df[["X"]]
df[[3]] <- NULL # deletion