martCheck - Error - You must provide a valid Mart object - for running HoneyBADGER for CNV computation

Question

[mete.han.celebi]

Hello everyone,

I have a seurat object where I defined the cells as immune cells based on their AUCell scores so that I could use them as a normal cell to compute the CNVs of malignant cells. For that purpose I use the HoneyBADGER. However, when running the HoneyBADGER, I am running a problem regarding the biomaRt.

Here is my codes:

# Create the object
hb <- new("HoneyBADGER", name = "Malignant_CNVs")
hb$setGexpMats(as.matrix(tumor_counts), normal_ref,
           filter = TRUE, scale = FALSE, verbose = TRUE)

Then I got this error:

Initializing expression matrices ... 
13642 genes passed filtering ... 
Normalizing gene expression for 13642 genes and 12243 cells ... 
Error in martCheck(mart) : 
You must provide a valid Mart object. To create a Mart object use the function: useMart.  Check ?useMart for more information.
In addition: Warning message:
In asMethod(object) :
sparse->dense coercion: allocating vector of size 1.5 GiB

I would be more than happy if you could help me out to fix that error.

Thank you very much in advance! Metehan

Answer 1

[mete.han.celebi]

Hello everyone,

I have fixed the issue.

Here how I fixed:

mart.obj <- useMart(
biomart = "ENSEMBL_MART_ENSEMBL",
dataset = "hsapiens_gene_ensembl"
)

hb <- new("HoneyBADGER", name = "Malignant_CNVs")
# Set tumor and reference expression
hb$setGexpMats(
tumor_counts,
normal_ref,
mart.obj,          # <-- key addition
filter = FALSE,
scale = FALSE,
verbose = TRUE
)