Mutual Nearest Neighbor Batch correction not working

[IkjotSidhu]

I am not able to use the MNN method right now, Here is my code followed by the error-

# Create iCellR object here
my.obj <- make.obj(ag.data)

# QC
my.obj <- qc.stats(my.obj,
s.phase.genes = s.phase, 
g2m.phase.genes = g2m.phase)

# filter
my.obj <- cell.filter(my.obj)
my.obj <- gene.stats(my.obj, which.data = "main.data")

my.obj <- make.gene.model(my.obj, my.out.put = "data",
    dispersion.limit = 1.5,
    base.mean.rank = 500,
    no.mito.model = T,
    mark.mito = T,
    interactive = F,
    no.cell.cycle = T,
    out.name = "gene.model")

library(scran)
library(BiocNeighbors)
my.obj <- run.mnn(my.obj,
    method = "gene.model",
    gene.list = my.obj@gene.model,
    k=20,
    d=50)

Prepering samples ... Running fast MNN ... 'fastMNN' is deprecated. Use 'batchelor::fastMNN' instead. 'package:stats' may not be available when loading'package:stats' may not be available when loading'package:stats' may not be available when loading'package:stats' may not be available when loading'package:stats' may not be available when loadingpackage:stats' may not be available when loading'package:stats' may not be available when loadingError in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘queryKNN’ for signature ‘"missing", "NULL"’

[rezakj]

Update iCellR by CRAN and run it again.

[IkjotSidhu]

It failed again. The same error as before.

[rezakj]

It's the version of SCRAN.

Here is my session info. If you install it in R 3.5 it should work. You need a version of scran that has the fastMNN function. Mine is scran_1.10.2

In the near future I will fix this. But for now, let me know if this fixes the error!

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS: /gpfs/share/apps/R/3.5.1/lib64/R/lib/libRblas.so
LAPACK: /gpfs/share/apps/R/3.5.1/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] scran_1.10.2                SingleCellExperiment_1.4.1
 [3] SummarizedExperiment_1.12.0 DelayedArray_0.8.0
 [5] matrixStats_0.55.0          Biobase_2.42.0
 [7] GenomicRanges_1.34.0        GenomeInfoDb_1.18.2
 [9] IRanges_2.16.0              S4Vectors_0.20.1
[11] BiocGenerics_0.28.0         BiocParallel_1.16.6

loaded via a namespace (and not attached):
 [1] statmod_1.4.32           beeswarm_0.2.3           locfit_1.5-9.1
 [4] tidyselect_0.2.5         reshape2_1.4.3           purrr_0.3.3
 [7] HDF5Array_1.10.1         lattice_0.20-38          rhdf5_2.26.2
[10] colorspace_1.4-1         viridisLite_0.3.0        rlang_0.4.0
[13] pillar_1.4.2             glue_1.3.1               GenomeInfoDbData_1.2.0
[16] plyr_1.8.4               stringr_1.4.0            zlibbioc_1.28.0
[19] munsell_0.5.0            gtable_0.3.0             vipor_0.4.5
[22] scater_1.10.1            BiocNeighbors_1.0.0      Rcpp_1.0.2
[25] edgeR_3.24.3             scales_1.0.0             limma_3.38.3
[28] XVector_0.22.0           gridExtra_2.3            ggplot2_3.2.1
[31] stringi_1.4.3            dplyr_0.8.3              grid_3.5.1
[34] tools_3.5.1              bitops_1.0-6             magrittr_1.5
[37] RCurl_1.95-4.12          lazyeval_0.2.2           tibble_2.1.3
[40] dynamicTreeCut_1.63-1    crayon_1.3.4             pkgconfig_2.0.3
[43] Matrix_1.2-17            DelayedMatrixStats_1.4.0 ggbeeswarm_0.6.0
[46] assertthat_0.2.1         viridis_0.5.1            Rhdf5lib_1.4.3
[49] R6_2.4.0                 igraph_1.2.4.1           compiler_3.5.1