1. MineICA
  2. Commit 863b53ab05ea4064c61a6fec2beedb4bda33256d
Browse code

resolve Windows warnings occuring in the build 'file link 'MineICAParams-class' in package 'MineICA' does not exist and so has been treated as a topic'

Anne Biton authored on 23/04/2020 18:30:14
Showing 18 changed files
man/Alist.Rd
History View file @ 863b53a
... ... 
@@ -23,4 +23,4 @@ Alist(object)
23 23 
 }
24 24 
 \author{Anne Biton}
25 25
26 
-\seealso{\code{\link{IcaSet-class}}}
26 
+\seealso{\code{\link{class-IcaSet}}}
man/Slist.Rd
History View file @ 863b53a
... ... 
@@ -25,4 +25,4 @@ SlistByGene(object)
25 25 
 }
26 26 
 \author{Anne Biton}
27 27
28 
-\seealso{\code{\link{IcaSet-class}}}
28 
+\seealso{\code{\link{class-IcaSet}}}
man/buildMineICAParams.Rd
History View file @ 863b53a
... ... 
@@ -47,11 +47,11 @@
47 47 
 }
48 48 
 \description{
49 49 
   This function builds an object of class
50 
-  \code{\link[MineICA:MineICAParams-class]{MineICAParams}}.
50 
+  \code{\link[MineICA:class-MineICAParams]{MineICAParams}}.
51 51 
   It contains the parameters that will be used by function
52 52 
   \code{\link{runAn}} to analyze the ICA decomposition
53 53 
   contained in an object of class
54 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}.
54 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}.
55 55 
 }
56 56 
 \examples{
57 57 
 ## define default parameters and fill resPath
... ... 
@@ -64,7 +64,7 @@ params <- buildMineICAParams(resPath="resMineICACarbayo/", selCutoff=4)
64 64 
   Anne Biton
65 65 
 }
66 66 
 \seealso{
67 
-  \code{\link[MineICA:MineICAParams-class]{MineICAParams}},
67 
+  \code{\link[MineICA:class-MineICAParams]{MineICAParams}},
68 68 
   \code{\link[MineICA]{runAn}}
69 69 
 }
70 70
man/build_sortHeatmap.Rd
History View file @ 863b53a
... ... 
@@ -42,7 +42,7 @@
42 42 
   This function returns the matrices that will be used to
43 43 
   plot the heatmaps of each component. It restricts the
44 44 
   data matrix of the
45 
-  \code{\link[MineICA:IcaSet-class]{icaSet}} object to the
45 
+  \code{\link[MineICA:class-IcaSet]{icaSet}} object to the
46 46 
   contributing genes/features, and order the features/genes
47 47 
   and samples.
48 48 
 }
man/class-IcaSet.Rd
History View file @ 863b53a
... ... 
@@ -318,7 +318,7 @@
318 318
319 319 
 \seealso{
320 320 
   \code{\link{eSet-class}}, \code{\link{buildIcaSet}},
321 
-  \code{\link{IcaSet-class}}, \code{\link{MineICAParams-class}}.
321 
+  \code{\link{class-IcaSet}}, \code{\link{class-MineICAParams}}.
322 322 
 }
323 323
324 324 
 \examples{
man/class-MineICAParams.Rd
History View file @ 863b53a
... ... 
@@ -2,7 +2,7 @@
2 2 
 \docType{class}
3 3 
 \alias{class:MineICAParams}
4 4 
 \alias{MineICAParams}
5 
-\alias{MineICAParams-class}
5 
+\alias{class-MineICAParams}
6 6 
 \alias{Sfile}
7 7 
 \alias{getSfile}
8 8 
 \alias{setSfile}
... ... 
@@ -139,7 +139,7 @@
139 139 
 \author{Anne Biton}
140 140
141 141 
 \seealso{
142 
-  \code{\link{MineICAParams-class}}, \code{\link{runAn}}.
142 
+  \code{\link{class-MineICAParams}}, \code{\link{runAn}}.
143 143 
 }
144 144
145 145 
 \examples{
man/clusVarAnalysis.Rd
History View file @ 863b53a
... ... 
@@ -13,10 +13,10 @@
13 13 
 }
14 14 
 \arguments{
15 15 
   \item{icaSet}{An object of class
16 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}}
16 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}}
17 17
18 18 
   \item{params}{An object of class
19 
-  \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
19 
+  \code{\link[MineICA:class-MineICAParams]{MineICAParams}}
20 20 
   providing the parameters of the analysis}
21 21
22 22 
   \item{resClus}{A list of numeric vectors indexed by
man/getComp.Rd
History View file @ 863b53a
... ... 
@@ -30,4 +30,4 @@ getComp(object, level, ind)
30 30 
 }
31 31 
 \author{Anne Biton}
32 32
33 
-\seealso{\code{\link{IcaSet-class}}}
33 
+\seealso{\code{\link{class-IcaSet}}}
man/hypergeoAn.Rd
History View file @ 863b53a
... ... 
@@ -11,7 +11,7 @@
11 11 
   \item{icaSet}{An object of class \code{IcaSet}}
12 12
13 13 
   \item{params}{An object of class
14 
-  \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
14 
+  \code{\link[MineICA:class-MineICAParams]{MineICAParams}}
15 15 
   containing the parameters of the analysis}
16 16
17 17 
   \item{path}{The path where results will be saved}
... ... 
@@ -50,7 +50,7 @@
50 50 
   Runs an enrichment analysis of the contributing genes
51 51 
   associated with each component, using the function
52 52 
   \code{hyperGTest} of package
53 
-  \code{\link[GOstats]{GOstats}}. The easiest way to run
53 
+  \code{\link{GOstats}}. The easiest way to run
54 54 
   enrichment analysis is to use function
55 55 
   \code{\link{runEnrich}}.
56 56 
 }
man/plotDensAllAnnotInAllComp.Rd
History View file @ 863b53a
... ... 
@@ -11,10 +11,10 @@
11 11 
 }
12 12 
 \arguments{
13 13 
   \item{icaSet}{an object of class
14 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}}
14 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}}
15 15
16 16 
   \item{params}{An object of the class
17 
-  \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
17 
+  \code{\link[MineICA:class-MineICAParams]{MineICAParams}}
18 18 
   containing the parameters of the analysis}
19 19
20 20 
   \item{path}{the directory where the plots will be
man/plotDensOneAnnotInAllComp.Rd
History View file @ 863b53a
... ... 
@@ -9,7 +9,7 @@
9 9 
 }
10 10 
 \arguments{
11 11 
   \item{icaSet}{an object of class
12 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}}
12 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}}
13 13
14 14 
   \item{keepVar}{a variable label, i.e the label of a
15 15 
   column of the pheno data of icaSet available in
man/plotPosAnnotInComp.Rd
History View file @ 863b53a
... ... 
@@ -77,7 +77,7 @@
77 77 
   This function plots the positions of groups of samples
78 78 
   formed by the variables (i.e the sample annotations)
79 79 
   across all the components of an object of class
80 
-  \code{\link[MineICA:IcaSet-class]{icaSet}}. For each
80 
+  \code{\link[MineICA:class-IcaSet]{icaSet}}. For each
81 81 
   variable level (e.g for each tumor stage) this function
82 82 
   plots the positions of the corresponding samples (e.g the
83 83 
   subset of samples having this tumor stage) within the
man/plotPosSamplesInComp.Rd
History View file @ 863b53a
... ... 
@@ -19,7 +19,7 @@
19 19 
   \code{names(samplesByGroup)} is NULL.}
20 20
21 21 
   \item{icaSet}{An object of class
22 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}}
22 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}}
23 23
24 24 
   \item{keepComp}{A subset of components available in
25 25 
   \code{indComp(icaSet)}, if NULL (default) all components
... ... 
@@ -57,7 +57,7 @@
57 57 
 \description{
58 58 
   This function plots the positions of several groups of
59 59 
   samples across all the components of an
60 
-  \code{\link[MineICA:IcaSet-class]{icaSet}} object.
60 
+  \code{\link[MineICA:class-IcaSet]{icaSet}} object.
61 61 
 }
62 62 
 \details{
63 63 
   For each subgroup of samples this function plots their
... ... 
@@ -98,7 +98,7 @@ dev.off()
98 98 
 }
99 99 
 \seealso{
100 100 
   \code{\link{hist}},
101 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}
101 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}
102 102 
 }
103 103 
 \keyword{internal}
104 104
man/qualVarAnalysis.Rd
History View file @ 863b53a
... ... 
@@ -14,11 +14,11 @@
14 14 
 }
15 15 
 \arguments{
16 16 
   \item{params}{An object of class
17 
-  \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
17 
+  \code{\link[MineICA:class-MineICAParams]{MineICAParams}}
18 18 
   providing the parameters of the analysis.}
19 19
20 20 
   \item{icaSet}{An object of class
21 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}.}
21 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}.}
22 22
23 23 
   \item{keepVar}{The variable labels to be considered, must
24 24 
   be a subset of \code{varLabels(icaSet)}.}
man/quantVarAnalysis.Rd
History View file @ 863b53a
... ... 
@@ -14,11 +14,11 @@
14 14 
 }
15 15 
 \arguments{
16 16 
   \item{params}{An object of class
17 
-  \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
17 
+  \code{\link[MineICA:class-MineICAParams]{MineICAParams}}
18 18 
   providing the parameters of the analysis.}
19 19
20 20 
   \item{icaSet}{An object of class
21 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}.}
21 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}.}
22 22
23 23 
   \item{keepVar}{The variable labels to be considered, must
24 24 
   be a subset of \code{varLabels(icaSet)}.}
man/runAn.Rd
History View file @ 863b53a
... ... 
@@ -19,11 +19,11 @@
19 19 
 }
20 20 
 \arguments{
21 21 
   \item{params}{An object of class
22 
-  \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
22 
+  \code{\link[MineICA:class-MineICAParams]{MineICAParams}}
23 23 
   containing the parameters of the analysis.}
24 24
25 25 
   \item{icaSet}{An object of class
26 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}.}
26 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}.}
27 27
28 28 
   \item{keepVar}{The variable labels to be considered, i.e
29 29 
   a subset of the annotation variables available in
... ... 
@@ -68,12 +68,12 @@
68 68
69 69 
   \item{ontoGOstats}{A string specifying the GO ontology to
70 70 
   use. Must be one of 'BP', 'CC', or 'MF', see
71 
-  \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.
71 
+  \code{\link[Category:class-GOHyperGParams]{GOHyperGParams}}.
72 72 
   Only used when argument \code{dbGOstats} is 'GO'.}
73 73
74 74 
   \item{condGOstats}{A logical indicating whether the
75 75 
   calculation should conditioned on the GO structure, see
76 
-  \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.}
76 
+  \code{\link[Category:class-GOHyperGParams]{GOHyperGParams}}.}
77 77
78 78 
   \item{cutoffGOstats}{The p-value threshold used for
79 79 
   selecting enriched gene sets, default is
man/runEnrich.Rd
History View file @ 863b53a
... ... 
@@ -8,10 +8,10 @@
8 8 
 }
9 9 
 \arguments{
10 10 
   \item{icaSet}{An object of class
11 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}}
11 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}}
12 12
13 13 
   \item{params}{An object of class
14 
-  \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
14 
+  \code{\link[MineICA:class-MineICAParams]{MineICAParams}}
15 15 
   providing the parameters of the analysis}
16 16
17 17 
   \item{dbs}{The database to use, default is
man/writeHtmlResTestsByAnnot.Rd
History View file @ 863b53a
... ... 
@@ -11,11 +11,11 @@
11 11 
 }
12 12 
 \arguments{
13 13 
   \item{params}{An object of class
14 
-  \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
14 
+  \code{\link[MineICA:class-MineICAParams]{MineICAParams}}
15 15 
   containing the parameters of the analysis}
16 16
17 17 
   \item{icaSet}{An object of class
18 
-  \code{\link[MineICA:IcaSet-class]{IcaSet}}}
18 
+  \code{\link[MineICA:class-IcaSet]{IcaSet}}}
19 19
20 20 
   \item{res}{A matrix or data.frame of dimension
21 21 
   'components x variables' containing numeric values that