1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
|
# S3 as.matrix method
as.matrix.DGEList <- function(x,...) as.matrix(x$counts)
# S3 as.data.frame method
as.data.frame.DGEList <- function(x,row.names=NULL,...)
# Created 17 June 2020.
{
if(is.null(x$genes)) {
data.frame(x$counts,row.names=row.names,check.rows=FALSE,check.names=FALSE,stringsAsFactors=FALSE)
} else {
if(is.null(row.names)) {
rn <- rownames(x$counts)
if(!is.null(rn) && !anyDuplicated(rn)) row.names(x$genes) <- rn
}
data.frame(x$genes,x$counts,row.names=row.names,check.rows=FALSE,check.names=FALSE,stringsAsFactors=FALSE)
}
}
as.data.frame.DGEExact <- as.data.frame.DGELRT <- function(x,row.names=NULL,...)
{
if(is.null(x$genes)) {
if(!is.null(row.names)) row.names(x$table) <- row.names
x$table
} else
data.frame(x$genes,x$table,row.names=row.names,check.rows=FALSE,check.names=FALSE,stringsAsFactors=FALSE)
}
as.data.frame.TopTags <- function(x,row.names=NULL,...)
{
if(!is.null(row.names)) row.names(x$table) <- row.names
x$table
}
# S3 dim methods
# These enable nrow() and ncol() as well
dim.DGEList <- function(x) if(is.null(x$counts)) c(0,0) else dim(as.matrix(x$counts))
dim.DGEGLM <- function(x) if(is.null(x$coefficients)) c(0,0) else dim(as.matrix(x$coefficients))
dim.DGEExact <- dim.TopTags <- dim.DGELRT <- function(x) if(is.null(x$table)) c(0,0) else dim(as.matrix(x$table))
# S3 length methods
# These methods have been removed so that edgeR objects will return list length instead of matrix length
#length.DGEList <- length.DGEExact <- length.TopTags <- length.DGEGLM <- length.DGELRT <- function(x) prod(dim(x))
# S3 dimnames methods
# These enable rownames() and colnames() as well
dimnames.DGEList <- function(x) dimnames(x$counts)
dimnames.DGEGLM <- function(x) dimnames(x$coefficients)
dimnames.DGEExact <- dimnames.DGELRT <- dimnames.TopTags <- function(x) dimnames(x$table)
# S3 dimnames<- methods
# These enable rownames()<- and colnames()<- as well
assign("dimnames<-.DGEList",function(x,value)
{
dimnames(x$counts) <- value
if(!is.null(x$samples)) row.names(x$samples) <- value[[2]]
if(!is.null(x$genes)) row.names(x$genes) <- value[[1]]
x
})
assign("dimnames<-.DGEExact",function(x,value)
{
dimnames(x$table) <- value
if(!is.null(x$genes)) row.names(x$genes) <- value[[1]]
x
})
assign("dimnames<-.DGEGLM",function(x,value)
{
dimnames(x$coefficients) <- value
if(!is.null(x$unshrunk.coefficients)) dimnames(x$unshrunk.coefficients) <- value
if(!is.null(x$fitted.values)) rownames(x$fitted.values) <- value[[1]]
if(!is.null(x$counts)) rownames(x$fitted.values) <- value[[1]]
if(!is.null(x$genes)) row.names(x$genes) <- value[[1]]
x
})
assign("dimnames<-.DGELRT",function(x,value)
# 4 June 2015
{
dimnames(x$table) <- value
if(!is.null(x$coefficients)) rownames(x$coefficients) <- value[[1]]
if(!is.null(x$unshrunk.coefficients)) rownames(x$unshrunk.coefficients) <- value[[1]]
if(!is.null(x$fitted.values)) rownames(x$fitted.values) <- value[[1]]
if(!is.null(x$counts)) rownames(x$fitted.values) <- value[[1]]
if(!is.null(x$genes)) row.names(x$genes) <- value[[1]]
x
})
# S3 head and tail methods
head.DGEList <- head.DGEExact <- head.DGEGLM <- head.DGELRT <- head.TopTags <-
function (x, n = 6L, ...)
{
stopifnot(length(n) == 1L)
n <- if (n < 0L)
max(nrow(x) + n, 0L)
else
min(n, nrow(x))
x[seq_len(n),]
}
tail.DGEList <- tail.DGEExact <- tail.DGEGLM <- tail.DGELRT <- tail.TopTags <-
function (x, n = 6L, ...)
{
stopifnot(length(n) == 1L)
nrx <- nrow(x)
n <- if (n < 0L)
max(nrx + n, 0L)
else
min(n, nrx)
x[seq.int(to = nrx, length.out = n),]
}
|
