could not find function "asDataFrame" about omixer-rpmr HOT 6 CLOSED

Hi Lara,

asDataFrame is a function in omixer-rpmR. Could you make sure the library is loaded before you call this function?
If this does not work please send the output of sessionInfo() and the script or the list of commands you are running before getting this error.

cheers,
Youssef

from omixer-rpmr.

Hi Youssef,

The library was indeed loaded. I am just running through the usage example you have provided for omixer-rpmR.

library(omixerRpm)
# read a functional profile matrix into R or create it inside R. Please note that row.names should not be used while reading the matrix. 
dat <- read.table("matrix.tsv", header=T, sep="\t")
# Run the module mapping on the loaded table.
mods <- rpm(dat, minimum.coverage=0.3, annotation = 1)

# alternatively run the mapping without loading the table into R.
mods <- rpm("matrix.tsv", minimum.coverage=0.3, annotation = 1)

# Load the default mapping database
db <- loadDefaultDB()
# get the name of the first predicted module
getNames(db, mods@annotation[1,])

# get the abundance|coverage as a data.frame with module id and description
coverage <- asDataFrame(mods, "coverage")

When the library is loaded I try to search the help for this function but receive the following error:

?asDataFrame
No documentation for ‘asDataFrame’ in specified packages and libraries:

Here is the output for sessionInfo()

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19

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       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] omixerRpm_0.3.1

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3  

Many thanks for your help,
Lara

from omixer-rpmr.

Could you please install this version of the library https://github.com/omixer/omixer-rpmR/releases/tag/0.3.1?
It should fix the problem. I messed up the versioning and indeed in the latest release asDataFrame is not a function.
The link I sent you was labeled as a pre-release and this is why you probably did not install it.
I hope this helps and if not I will spend more time on Monday to find a solution.

Best,
Youssef

from omixer-rpmr.

Still no luck with the new installation. But Monday sounds great.

Thanks again for your help.

Lara

from omixer-rpmr.

Hi Lara,

Indeed version 0.3.1 does not work. I released version 0.3.2 and tested it in a fresh docker environment to make sure asDataFrame is included in the package. This version will solve your problem!

Thank you so much for your feedback and please let me know if you face further issues using the library.

Best,
Youssef

from omixer-rpmr.

Success! Thank you Youssef.

Best,
Lara

from omixer-rpmr.