... | ... |
@@ -15,6 +15,7 @@ RoxygenNote: 7.1.2 |
15 | 15 |
biocViews: |
16 | 16 |
Imports: |
17 | 17 |
BiocGenerics, |
18 |
+ rlang, |
|
18 | 19 |
ggplot2, |
19 | 20 |
heatmaply, |
20 | 21 |
methods, |
... | ... |
@@ -22,12 +23,14 @@ Imports: |
22 | 23 |
stats |
23 | 24 |
Suggests: |
24 | 25 |
limma, |
26 |
+ Biobase, |
|
25 | 27 |
missForest, |
26 | 28 |
hexbin, |
27 | 29 |
Rtsne, |
28 | 30 |
vsn, |
29 | 31 |
VIM, |
30 | 32 |
pcaMethods, |
33 |
+ pls, |
|
31 | 34 |
testthat (>= 3.0.0) |
32 | 35 |
Depends: |
33 | 36 |
R (>= 3.6.0), |
... | ... |
@@ -45,26 +45,17 @@ export(.set_poplinReducedData_data_integer) |
45 | 45 |
export(.set_poplinReducedData_data_missing) |
46 | 46 |
export(.set_poplinReducedData_datalist) |
47 | 47 |
export(.verify_and_extract_input) |
48 |
-export(impute_halfmin) |
|
49 | 48 |
export(impute_knn) |
50 |
-export(impute_mean) |
|
51 |
-export(impute_median) |
|
52 | 49 |
export(impute_pca) |
53 | 50 |
export(impute_randomforest) |
54 | 51 |
export(impute_simple) |
55 |
-export(normalize_auto) |
|
56 | 52 |
export(normalize_cyclicloess) |
57 |
-export(normalize_euclidean) |
|
58 |
-export(normalize_level) |
|
59 | 53 |
export(normalize_mad) |
60 | 54 |
export(normalize_mean) |
61 | 55 |
export(normalize_median) |
62 |
-export(normalize_pareto) |
|
63 | 56 |
export(normalize_pqn) |
64 |
-export(normalize_range) |
|
65 | 57 |
export(normalize_scale) |
66 | 58 |
export(normalize_sum) |
67 |
-export(normalize_vast) |
|
68 | 59 |
export(normalize_vsn) |
69 | 60 |
export(poplin) |
70 | 61 |
export(poplinData) |
... | ... |
@@ -142,12 +142,6 @@ setGeneric( |
142 | 142 |
function(x, ...) standardGeneric("normalize_mad") |
143 | 143 |
) |
144 | 144 |
|
145 |
-##' @export |
|
146 |
-setGeneric( |
|
147 |
- "normalize_euclidean", |
|
148 |
- function(x, ...) standardGeneric("normalize_euclidean") |
|
149 |
-) |
|
150 |
- |
|
151 | 145 |
##' @export |
152 | 146 |
setGeneric( |
153 | 147 |
"normalize_cyclicloess", |
... | ... |
@@ -160,36 +154,6 @@ setGeneric( |
160 | 154 |
function(x, ...) standardGeneric("normalize_vsn") |
161 | 155 |
) |
162 | 156 |
|
163 |
-##' @export |
|
164 |
-setGeneric( |
|
165 |
- "normalize_auto", |
|
166 |
- function(x, ...) standardGeneric("normalize_auto") |
|
167 |
-) |
|
168 |
- |
|
169 |
-##' @export |
|
170 |
-setGeneric( |
|
171 |
- "normalize_range", |
|
172 |
- function(x, ...) standardGeneric("normalize_range") |
|
173 |
-) |
|
174 |
- |
|
175 |
-##' @export |
|
176 |
-setGeneric( |
|
177 |
- "normalize_pareto", |
|
178 |
- function(x, ...) standardGeneric("normalize_pareto") |
|
179 |
-) |
|
180 |
- |
|
181 |
-##' @export |
|
182 |
-setGeneric( |
|
183 |
- "normalize_vast", |
|
184 |
- function(x, ...) standardGeneric("normalize_vast") |
|
185 |
-) |
|
186 |
- |
|
187 |
-##' @export |
|
188 |
-setGeneric( |
|
189 |
- "normalize_level", |
|
190 |
- function(x, ...) standardGeneric("normalize_level") |
|
191 |
-) |
|
192 |
- |
|
193 | 157 |
##' @export |
194 | 158 |
setGeneric( |
195 | 159 |
"normalize_scale", |
... | ... |
@@ -213,24 +177,6 @@ setGeneric( |
213 | 177 |
function(x, ...) standardGeneric("impute_knn") |
214 | 178 |
) |
215 | 179 |
|
216 |
-##' @export |
|
217 |
-setGeneric( |
|
218 |
- "impute_halfmin", |
|
219 |
- function(x, ...) standardGeneric("impute_halfmin") |
|
220 |
-) |
|
221 |
- |
|
222 |
-##' @export |
|
223 |
-setGeneric( |
|
224 |
- "impute_median", |
|
225 |
- function(x, ...) standardGeneric("impute_median") |
|
226 |
-) |
|
227 |
- |
|
228 |
-##' @export |
|
229 |
-setGeneric( |
|
230 |
- "impute_mean", |
|
231 |
- function(x, ...) standardGeneric("impute_mean") |
|
232 |
-) |
|
233 |
- |
|
234 | 180 |
##' @export |
235 | 181 |
setGeneric( |
236 | 182 |
"impute_simple", |
... | ... |
@@ -13,14 +13,14 @@ |
13 | 13 |
##' |
14 | 14 |
##' Take a sequence of poplin objects in \code{...} and combine by rows. Note |
15 | 15 |
##' that all objects in ... must have the exact same values for |
16 |
-##' [poplin_data_list]. See \code{?}[rbind] for the interpretation of |
|
16 |
+##' \code{poplin_data_list}. See \code{?}[rbind] for the interpretation of |
|
17 | 17 |
##' \code{deparse.level}. |
18 | 18 |
##' |
19 | 19 |
##' } |
20 | 20 |
##' \item{\code{cbind(..., deparse.level = 1)}:}{ |
21 | 21 |
##' |
22 | 22 |
##' Take a sequence of poplin objects in \code{...} and combine by columns. Note |
23 |
-##' that all objects in ... must have the same values of [poplin_reduced_names]. |
|
23 |
+##' that all objects in ... must have the same values of \code{poplin_reduced_names}. |
|
24 | 24 |
##' Dimension reduction results with the same name across the objects will be |
25 | 25 |
##' combined row-wise to create the corresponding entry in the output object. |
26 | 26 |
##' See \code{?}[cbind] for the interpretation of \code{deparse.level}. |
... | ... |
@@ -44,8 +44,8 @@ |
44 | 44 |
##' be a logical, integer, character vector, or empty (missing). \code{value} |
45 | 45 |
##' must be a poplin object with the dimension and assay elements consistent |
46 | 46 |
##' with the subset \code{x[i, j]} being replaced. \code{value} is also expected |
47 |
-##' to have the same name and order of [poplin_data_names] (and |
|
48 |
-##' [poplin_reduced_names] as well if \code{j} is specified) as \code{x}.} |
|
47 |
+##' to have the same name and order of \code{poplin_data_names} (and |
|
48 |
+##' \code{poplin_reduced_names} as well if \code{j} is specified) as \code{x}.} |
|
49 | 49 |
##' |
50 | 50 |
##' } |
51 | 51 |
##' |
... | ... |
@@ -165,6 +165,9 @@ |
165 | 165 |
if (!requireNamespace("vsn", quietly = TRUE)) { |
166 | 166 |
stop("Package 'vsn' is required. Please install and try again.") |
167 | 167 |
} |
168 |
+ if (!requireNamespace("Biobase", quietly = TRUE)) { |
|
169 |
+ stop("Package 'Biobase' is required. Please install and try again.") |
|
170 |
+ } |
|
168 | 171 |
out <- suppressMessages(vsn::vsnMatrix(x = x, ...)) |
169 | 172 |
if (meanSdPlot) { |
170 | 173 |
if (!requireNamespace("hexbin", quietly = TRUE)) { |
... | ... |
@@ -19,14 +19,14 @@ In the code snippets below, \code{...} represents multiple |
19 | 19 |
|
20 | 20 |
Take a sequence of poplin objects in \code{...} and combine by rows. Note |
21 | 21 |
that all objects in ... must have the exact same values for |
22 |
-\link{poplin_data_list}. See \code{?}\link{rbind} for the interpretation of |
|
22 |
+\code{poplin_data_list}. See \code{?}\link{rbind} for the interpretation of |
|
23 | 23 |
\code{deparse.level}. |
24 | 24 |
|
25 | 25 |
} |
26 | 26 |
\item{\code{cbind(..., deparse.level = 1)}:}{ |
27 | 27 |
|
28 | 28 |
Take a sequence of poplin objects in \code{...} and combine by columns. Note |
29 |
-that all objects in ... must have the same values of \link{poplin_reduced_names}. |
|
29 |
+that all objects in ... must have the same values of \code{poplin_reduced_names}. |
|
30 | 30 |
Dimension reduction results with the same name across the objects will be |
31 | 31 |
combined row-wise to create the corresponding entry in the output object. |
32 | 32 |
See \code{?}\link{cbind} for the interpretation of \code{deparse.level}. |
... | ... |
@@ -52,8 +52,8 @@ indices specifying the rows and columns to extract or replace. Indices can |
52 | 52 |
be a logical, integer, character vector, or empty (missing). \code{value} |
53 | 53 |
must be a poplin object with the dimension and assay elements consistent |
54 | 54 |
with the subset \code{x[i, j]} being replaced. \code{value} is also expected |
55 |
-to have the same name and order of \link{poplin_data_names} (and |
|
56 |
-\link{poplin_reduced_names} as well if \code{j} is specified) as \code{x}.} |
|
55 |
+to have the same name and order of \code{poplin_data_names} (and |
|
56 |
+\code{poplin_reduced_names} as well if \code{j} is specified) as \code{x}.} |
|
57 | 57 |
|
58 | 58 |
} |
59 | 59 |
} |
... | ... |
@@ -2,6 +2,8 @@ |
2 | 2 |
% Please edit documentation in R/poplin.R |
3 | 3 |
\name{poplin-internals} |
4 | 4 |
\alias{poplin-internals} |
5 |
+\alias{poplinData} |
|
6 |
+\alias{poplinData<-} |
|
5 | 7 |
\title{Internal poplin fields} |
6 | 8 |
\description{ |
7 | 9 |
Methods to get or set internal fields in a \linkS4class{poplin} object. |