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
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
|
require(org.Hs.eg.db)
require(RUnit)
## map is just to represent a classic Bimap
map <- org.Hs.egSYMBOL
## map2 represents an AnnotationDbMap mapping made by some other process for BC
## map2 <- new("AnnotationDbMap", AnnotDb=org.Hs.eg.db, columns="SYMBOL")
map3 <- AnnotationDbi:::makeFlatBimapUsingSelect(org.Hs.eg.db, col="SYMBOL")
## And another map object expected by most other tests.
map2 <- AnnotationDbi:::makeFlatBimapUsingSelect(org.Hs.eg.db, col="ONTOLOGY")
##map3 <- AnnotationDbi:::flatten(map)
# molecular function, cellular component, biological process
bioconcepts <- c("MF", "CC", "BP")
## test ls
test_ls <- function(){
res <- ls(map)
checkTrue(is.character(res))
checkTrue(length(res) > 0)
checkEquals(c("1","10","100"), head(res,n=3))
res2 <- ls(map3)
checkTrue(is.character(res2))
checkTrue(length(res2) > 0)
checkEquals(c("1","10","100"), head(res2,n=3))
}
## test Lkeys and Rkeys
test_Lkeys <- function(){
lres <- Lkeys(map)
checkTrue(length(lres) >0)
checkTrue(!any(is.na(lres)))
checkTrue(length(lres) == length(unique(lres)))
lres2 <- Lkeys(map2)
checkTrue(length(lres2) >0)
checkTrue(!any(is.na(lres2)))
checkTrue(length(lres2) == length(unique(lres2)))
}
test_Rkeys <- function(){
rres <- Rkeys(map)
checkTrue(length(rres) >0)
checkTrue(!any(is.na(rres)))
checkTrue(length(rres) == length(unique(rres)))
rres2 <- Rkeys(map2)
checkTrue(length(rres2) >0)
checkTrue(!any(is.na(rres2)))
checkTrue(length(rres2) == length(unique(rres2)))
}
## test revmap (add a test now that it seems to work...
test_revmap <- function(){
rmap <- revmap(map)
checkTrue(rmap@direction == -1)
rmap2 <- revmap(map2)
checkTrue(rmap2@direction == -1)
}
## test mget
test_mget <- function(){
k <- c("1","2")
res <- mget(k, map)
checkEquals(names(res), k)
checkEquals(res[[1]], "A1BG")
checkTrue(length(res)==length(k))
res2 <- mget(k, map2)
checkEquals(names(res2), k)
checkTrue(setequal(res2[[1]], bioconcepts))
checkTrue(length(res2)==length(k))
## reverse test
kr <- c("CC","MF")
res3 <- mget(kr, revmap(map2))
checkEquals(names(res3), kr)
checkEquals(res3[[1]][1], "1")
checkTrue(length(res3)==length(kr))
}
## test as.list
test_as.list <- function(){
res <- as.list(map)
checkEquals(names(res)[1], "1")
checkEquals(res[[1]][1], "A1BG")
checkTrue(length(res)>1000)
res2 <- as.list(map2)
checkEquals(names(res2)[[1]], "1")
checkTrue(setequal(res2[[1]], bioconcepts))
checkTrue(length(res2)>1000)
## reverse test
res3 <- as.list(revmap(map2))
checkTrue(setequal(names(res3), bioconcepts))
checkEquals(res3[[1]][1], "1")
checkIdentical(length(res3), 3L)
}
## test as.character
test_as.character <- function(){
res <- as.character(map)
checkEquals(names(res)[1], "1")
checkEquals(res[[1]][1], "A1BG")
res2 <- as.character(map2)
checkEquals(names(res2[1:3]), rep("1", 3))
checkTrue(setequal(res2[names(res2) == "1"], bioconcepts))
## reverse test
res3 <- as.character(revmap(map2))
checkTrue(setequal(names(res3[res3 == "1"]), bioconcepts))
checkIdentical(unname(res3[1:3]), rep("1", 3))
}
## test eapply
test_eapply <- function(){
res <- eapply(map, length)
checkEquals(names(res)[1], "1")
checkTrue(res[[1]][1] == 1)
res2 <- eapply(map2, length)
checkEquals(names(res2)[1], "1")
checkTrue(res2[[1]][1] == 3)
}
## test get
test_get <- function(){
k <- "1"
res <- get(k, map)
checkTrue(res == "A1BG")
res2 <- get(k, map2)
checkTrue(setequal(res2, bioconcepts))
## reverse test
kr <- "CC"
res3 <- get(kr, revmap(map2))
checkTrue(res3[[1]][1] == "1")
}
## test exists
test_exists <- function(){
checkTrue(exists("2", map) == TRUE)
checkTrue(exists("titi", map) == FALSE)
checkTrue(exists("9", map2) == TRUE)
checkTrue(exists("titi", map2) == FALSE)
}
## test "[["
test_dblBrackets <- function(){
res <- map[["1"]]
checkTrue(res == "A1BG")
res2 <- map2[["1"]]
checkTrue(setequal(res2, bioconcepts))
}
test_head <- function(){
res <- head(map, n=3)
checkTrue( class(res) == "AnnDbBimap" )
res2 <- head(map2, n=3) ## implement Lkeys and Rkeys
checkTrue( class(res2) == "data.frame" )
checkTrue( dim(res2)[1] == 3 )
checkTrue( dim(res2)[2] == 2 )
}
test_tail <- function(){
res <- tail(map, n=3)
checkTrue( class(res) == "AnnDbBimap" )
res2 <- tail(map2, n=3)
checkTrue( class(res2) == "data.frame" )
checkTrue( dim(res2)[1] == 3 )
checkTrue( dim(res2)[2] == 2 )
}
## test "$"
test_Dollar <- function(){
res <- map$"1"
checkTrue(res == "A1BG")
res2 <- map2$"1"
checkTrue(setequal(res2, bioconcepts))
}
## test toTable as.data.frame
test_toTable <- function(){
res <- toTable(map)
resdf <- as.data.frame(map)
checkEquals(res, resdf)
checkEquals(colnames(res), c("gene_id","symbol"))
checkTrue(res[1,1]==1)
checkTrue(res[1,2]=="A1BG")
## So one potential issue I have is that I get the "wrong" sort of headings?
## this is largely a cosmetic issue though...
res2 <- toTable(map2)
resdf2 <- as.data.frame(map2)
checkEquals(res2, resdf2)
checkEquals(colnames(res2), c("ENTREZID","ONTOLOGY"))
checkTrue(res2[1,1]==1)
checkTrue(
setequal(res2[res2[["ENTREZID"]]==1, "ONTOLOGY"], bioconcepts)
)
}
test_sample <- function(){
res <- sample(map,size=2)
checkTrue(length(res)==2)
checkTrue(class(res)=="list")
res2 <- sample(map2,size=2)
checkTrue(length(res2)==2)
checkTrue(class(res2)=="list")
}
|
