Could not find function "impute_met_state"

[ibulanov]

Hi there,

I tried to pass the vignette 'Cluster and impute scBS-seq...' and when I try to run the evaluating imputation performance:

imputation_obj <- impute_met_state(obj = melissa_obj, test = dt_obj$met_test)

I get the error:

Error in impute_met_state(obj = melissa_obj, test = dt_obj$met_test) : could not find function "impute_met_state"

Of course, I imported both Melissa and BPRMeth packages.

Have you deleted or move this function? Thanks in advance!

Best,
Igor

My sessionInfo():

R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19.3

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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

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

other attached packages:
[1] Melissa_1.5.3 BPRMeth_1.15.3 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
[7] BiocGenerics_0.34.0 RMySQL_0.10.20 DBI_1.1.0

[andreaskapou]

Hi Igor,

After updating the package (you are using the latest development version) I changed the function name, although I should have deprecated the old one. Apologies for that.

The new command for imputing methylation data (after having partitioned the data to train and test set) is:
imputation_obj <- impute_test_met(obj = melissa_obj, test = dt_obj$met_test)

Please see the updated vignette here: https://rpubs.com/cakapourani/melissa-analysis

Hope this helps!

Best,
Andreas

[andreaskapou]

Assuming this is resolved and closing issue.