Obtain the feature module of a feature of interest

This function will output the gene module of a specific gene(s) from a celda model

# S3 method for celda_CG
featureModuleLookup(counts, celda.mod, feature,
  exact.match = TRUE)

Arguments

counts	Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate `celda.mod`.
celda.mod	Model of class "celda_G" or "celda_CG".
feature	Character vector. Identify feature modules for the specified feature names.
exact.match	Logical. Whether to look for exact match of the gene name within counts matrix. Default TRUE.

Value

List. Each entry corresponds to the feature module determined for the provided features

Examples

celda.sim = simulateCells("celda_CG")
celda.mod = celda_CG(celda.sim$counts, K=celda.sim$K, L=celda.sim$L)
#> --------------------------------------------------------------------
#> Starting Celda_CG: Clustering cells and genes.
#> --------------------------------------------------------------------
#> Thu Sep 06 12:57:03 2018 .. Initializing chain 1 with 'random' (seed=12345)
#> Thu Sep 06 12:57:03 2018 .... Completed iteration: 1 | logLik: -1302242.28026966
#> Thu Sep 06 12:57:03 2018 .... Completed iteration: 2 | logLik: -1270044.02532694
#> Thu Sep 06 12:57:03 2018 .... Completed iteration: 3 | logLik: -1262209.15789703
#> Thu Sep 06 12:57:03 2018 .... Completed iteration: 4 | logLik: -1261712.35040107
#> Thu Sep 06 12:57:03 2018 .... Completed iteration: 5 | logLik: -1261712.57070977
#> Thu Sep 06 12:57:03 2018 .... Completed iteration: 6 | logLik: -1261711.00382116
#> Thu Sep 06 12:57:03 2018 .... Completed iteration: 7 | logLik: -1261716.24159949
#> Thu Sep 06 12:57:03 2018 .... Completed iteration: 8 | logLik: -1261479.73933942
#> Thu Sep 06 12:57:03 2018 .... Completed iteration: 9 | logLik: -1259874.14368698
#> Thu Sep 06 12:57:03 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:03 2018 .... Cluster 1 was reassigned and cluster 4 was split in two.
#> Thu Sep 06 12:57:03 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:04 2018 .... Cluster 2 was reassigned and cluster 9 was split in two.
#> Thu Sep 06 12:57:04 2018 .... Completed iteration: 10 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:04 2018 .... Completed iteration: 11 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:04 2018 .... Completed iteration: 12 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:04 2018 .... Completed iteration: 13 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:04 2018 .... Completed iteration: 14 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:04 2018 .... Completed iteration: 15 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:04 2018 .... Completed iteration: 16 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:04 2018 .... Completed iteration: 17 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:04 2018 .... Completed iteration: 18 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:04 2018 .... Completed iteration: 19 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:04 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:05 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:05 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:06 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:06 2018 .... Completed iteration: 20 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:06 2018 .. Finished chain 1 with seed 12345
#> Thu Sep 06 12:57:06 2018 .. Initializing chain 2 with 'random' (seed=12346)
#> Thu Sep 06 12:57:06 2018 .... Completed iteration: 1 | logLik: -1288484.90567663
#> Thu Sep 06 12:57:06 2018 .... Completed iteration: 2 | logLik: -1252316.73202744
#> Thu Sep 06 12:57:06 2018 .... Completed iteration: 3 | logLik: -1250339.95568952
#> Thu Sep 06 12:57:06 2018 .... Completed iteration: 4 | logLik: -1249564.71677654
#> Thu Sep 06 12:57:06 2018 .... Completed iteration: 5 | logLik: -1249563.6294892
#> Thu Sep 06 12:57:06 2018 .... Completed iteration: 6 | logLik: -1249564.31589985
#> Thu Sep 06 12:57:06 2018 .... Completed iteration: 7 | logLik: -1249563.24732323
#> Thu Sep 06 12:57:06 2018 .... Completed iteration: 8 | logLik: -1249563.4198964
#> Thu Sep 06 12:57:06 2018 .... Completed iteration: 9 | logLik: -1249563.4198964
#> Thu Sep 06 12:57:06 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:06 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:06 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:07 2018 .... Cluster 1 was reassigned and cluster 5 was split in two.
#> Thu Sep 06 12:57:07 2018 .... Completed iteration: 10 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:07 2018 .... Completed iteration: 11 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:07 2018 .... Completed iteration: 12 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:07 2018 .... Completed iteration: 13 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:07 2018 .... Completed iteration: 14 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:07 2018 .... Completed iteration: 15 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:07 2018 .... Completed iteration: 16 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:08 2018 .... Completed iteration: 17 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:08 2018 .... Completed iteration: 18 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:08 2018 .... Completed iteration: 19 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:08 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:08 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:08 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:10 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:10 2018 .... Completed iteration: 20 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:10 2018 .. Finished chain 2 with seed 12346
#> Thu Sep 06 12:57:10 2018 .. Initializing chain 3 with 'random' (seed=12347)
#> Thu Sep 06 12:57:10 2018 .... Completed iteration: 1 | logLik: -1272446.65246189
#> Thu Sep 06 12:57:10 2018 .... Completed iteration: 2 | logLik: -1251530.86145074
#> Thu Sep 06 12:57:10 2018 .... Completed iteration: 3 | logLik: -1251528.38544994
#> Thu Sep 06 12:57:10 2018 .... Completed iteration: 4 | logLik: -1251523.68686302
#> Thu Sep 06 12:57:10 2018 .... Completed iteration: 5 | logLik: -1251527.44696783
#> Thu Sep 06 12:57:10 2018 .... Completed iteration: 6 | logLik: -1251522.13351871
#> Thu Sep 06 12:57:10 2018 .... Completed iteration: 7 | logLik: -1251526.73996701
#> Thu Sep 06 12:57:10 2018 .... Completed iteration: 8 | logLik: -1251529.06808316
#> Thu Sep 06 12:57:10 2018 .... Completed iteration: 9 | logLik: -1251527.40248727
#> Thu Sep 06 12:57:10 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:11 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:11 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:11 2018 .... Cluster 1 was reassigned and cluster 5 was split in two.
#> Thu Sep 06 12:57:11 2018 .... Completed iteration: 10 | logLik: -1248422.30438372
#> Thu Sep 06 12:57:11 2018 .... Completed iteration: 11 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:11 2018 .... Completed iteration: 12 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:11 2018 .... Completed iteration: 13 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:11 2018 .... Completed iteration: 14 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:11 2018 .... Completed iteration: 15 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:11 2018 .... Completed iteration: 16 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:11 2018 .... Completed iteration: 17 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:11 2018 .... Completed iteration: 18 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:11 2018 .... Completed iteration: 19 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:11 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:12 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:12 2018 .... Completed iteration: 20 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:12 2018 .... Determining if any cell clusters should be split.
#> Thu Sep 06 12:57:12 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:12 2018 .... Determining if any gene clusters should be split.
#> Thu Sep 06 12:57:13 2018 .... No additional splitting was performed.
#> Thu Sep 06 12:57:13 2018 .... Completed iteration: 21 | logLik: -1248355.63470669
#> Thu Sep 06 12:57:13 2018 .. Finished chain 3 with seed 12347
#> --------------------------------------------------------------------
#> Completed Celda_CG. Total time: 10.59193 secs
#> --------------------------------------------------------------------
module = featureModuleLookup(celda.sim$counts, celda.mod, c("Gene_1", "Gene_XXX"))