I have recently started to work with the "qsea" package in r for differential methylation analysis between two groups with data derived from MeDIP-seq.

I input my bam files and created a data.frame("dataframe") accordingly, example:

sample_name     file_name   group
A1                          "A1.bam"            A
B1                          "B1.bam"            B
A2                          "A2.bam"            A

When I try to create a qseaSet

seaSet=createQseaSet(sampleTable=dataframe, BSgenome="BSgenome.Hsapiens.UCSC.hg38",  chr.select=NULL,  window_size=500))

the following error appears:

"Error in as.character.default(X[[i]], ...) :  no method for coercing this S4 class to a vector”

Is there anyone acquainted with the "qsea" package that can help me with this? Thank you,

Ricardo Ferreira (PhD student, ICBAS, University of Porto, Portugal)