... | ... |
@@ -154,6 +154,7 @@ setMethod("decontX", "SingleCellExperiment", function(x, |
154 | 154 |
batch = NULL, |
155 | 155 |
background = NULL, |
156 | 156 |
bgAssayName = NULL, |
157 |
+ bgBatch = NULL, |
|
157 | 158 |
maxIter = 500, |
158 | 159 |
delta = c(10, 10), |
159 | 160 |
estimateDelta = TRUE, |
... | ... |
@@ -182,6 +183,7 @@ setMethod("decontX", "SingleCellExperiment", function(x, |
182 | 183 |
z = z, |
183 | 184 |
batch = batch, |
184 | 185 |
countsBackground = countsBackground, |
186 |
+ batchBackground = bgBatch, |
|
185 | 187 |
maxIter = maxIter, |
186 | 188 |
convergence = convergence, |
187 | 189 |
iterLogLik = iterLogLik, |
... | ... |
@@ -234,6 +236,7 @@ setMethod("decontX", "ANY", function(x, |
234 | 236 |
z = NULL, |
235 | 237 |
batch = NULL, |
236 | 238 |
background = NULL, |
239 |
+ bgBatch = NULL, |
|
237 | 240 |
maxIter = 500, |
238 | 241 |
delta = c(10, 10), |
239 | 242 |
estimateDelta = TRUE, |
... | ... |
@@ -257,6 +260,7 @@ setMethod("decontX", "ANY", function(x, |
257 | 260 |
z = z, |
258 | 261 |
batch = batch, |
259 | 262 |
countsBackground = countsBackground, |
263 |
+ batchBackground = bgBatch, |
|
260 | 264 |
maxIter = maxIter, |
261 | 265 |
convergence = convergence, |
262 | 266 |
iterLogLik = iterLogLik, |
... | ... |
@@ -339,6 +343,7 @@ setMethod( |
339 | 343 |
z = NULL, |
340 | 344 |
batch = NULL, |
341 | 345 |
countsBackground = NULL, |
346 |
+ batchBackground = NULL, |
|
342 | 347 |
maxIter = 200, |
343 | 348 |
convergence = 0.001, |
344 | 349 |
iterLogLik = 10, |
... | ... |
@@ -369,6 +374,7 @@ setMethod( |
369 | 374 |
runParams <- list( |
370 | 375 |
z = z, |
371 | 376 |
batch = batch, |
377 |
+ batchBackground = batchBackground, |
|
372 | 378 |
maxIter = maxIter, |
373 | 379 |
delta = delta, |
374 | 380 |
estimateDelta = estimateDelta, |
... | ... |
@@ -398,6 +404,7 @@ setMethod( |
398 | 404 |
## Generate batch labels if none were supplied |
399 | 405 |
if (is.null(batch)) { |
400 | 406 |
batch <- rep("all_cells", nC) |
407 |
+ batchBackground <- rep("all_cells", ncol(countsBackground)) |
|
401 | 408 |
} |
402 | 409 |
runParams$batch <- batch |
403 | 410 |
batchIndex <- unique(batch) |