tallulandrews / m3d Goto Github PK

Dear Tallulah,

thanks for the nice package and the nice paper. During installation, numDeriv was additionally required for me. Maybe you can add it to the DESCRIPTION file in one of the next updates to smooth-en the installation process.

Best,
Jens

library(M3DExampleData)
Normalized_data <- M3DropCleanData(Mmus_example_list$data,
labels = Mmus_example_list$labels,
is.counts=TRUE, min_detected_genes=2000)
DE_genes <- M3DropFeatureSelection(Normalized_data$data,
mt_method="fdr", mt_threshold=0.01)

Error in M3DropFeatureSelection(Normalized_data$data, mt_method = "fdr", :
could not find function "M3DropFeatureSelection"

Q. why can't find the M3DropFeatureSelection function??

Thanks in advance.!

Hi,

I was not able to install the latest devel version of M3Drop (version1.93) because this version requires R 3.6. It seems that M3Drop (version 1.80) does not have functions for UMI data, so I installed the github version 3.10.3. My question is does this github version 3.10.3 correspond to Bioconductor version 1.93?

Best,
Danshu

This can be seen by running:

library(M3Drop)
library(M3DExampleData)
head(M3DropFeatureSelection(Mmus_example_list$data))
                     Gene effect.size       p.value       q.value
Zbed3              Ythdf1    185.4357 5.007261e-106 8.856844e-102
Klf17                Klf1    173.3116  5.044574e-92  8.922843e-88
C86187             C78339    161.8889  2.987961e-90  5.285106e-86
Btg4                 Btg1    150.8926  1.062441e-71  1.879246e-67
LOC100502936 LOC100233207    136.2464  1.932114e-32  3.417523e-28
Oog3                  Omd    131.4741  4.421721e-67  7.821140e-63
Warning message:
In bg__calc_variables(expr_mat) : Warning: Removing 18 invariant genes.

As you can see, the rownames and the Gene column do not agree. The rownames appear to be correct, which can be seen by removing the zeros before running M3DropFeatureSelection:

head(M3DropFeatureSelection(Mmus_example_list$data[rowSums(Mmus_example_list$data) > 0, ]))
                     Gene effect.size       p.value       q.value
Zbed3               Zbed3    185.4357 5.007261e-106 8.856844e-102
Klf17               Klf17    173.3116  5.044574e-92  8.922843e-88
C86187             C86187    161.8889  2.987961e-90  5.285106e-86
Btg4                 Btg4    150.8926  1.062441e-71  1.879246e-67
LOC100502936 LOC100502936    136.2464  1.932114e-32  3.417523e-28
Oog3                 Oog3    131.4741  4.421721e-67  7.821140e-63

This could be fixed potentially by checking for zero rows and removing them (with a warning) as the first step in M3DropFeatureSelection.

Best,
Brian