GeorgescuC
commented
1 year ago Hi @Dana11T ,
The "run.final.infercnv_obj" is a copy/backup of the infercnv object as is returned at the end of the analysis. It contains all the information used to generate the other outputs (except the HMM outputs as those are stored in the HMM object backups):
- the residual expression matrix in
@expr.data - the gene table in
@gene_order* - the indices of references and observations per annotation in
@reference_grouped_cell_indicesand@observation_grouped_cell_indicesrespectively - the hclust and subclustering information in
@tumor_subclusters
If you are simply interested in the "infercnv.observations.txt" and "infercnv.references.txt" outputs, you can add the write_expr_matrix=TRUE argument to the infercnv::run() call or to a plot_cnv() call to have them generated again. They have been disabled by default as it lengthens the plotting process and disk usage can quickly climb if generating more than a single figure.
If you need more information, please let me know.
Regards, Christophe.
I recently used a new server for infercnv analysis and noticed that the output files were different from the previous versions. The files "infercnv.observations.txt" and "infercnv.references.txt" were missing, and instead, a new object called "run.final.infercnv_obj" appeared. Through my search, I found that "run.final.infercnv_obj@expr.data" may contain CNV information. I would like to know what information is included in "run.final.infercnv_obj", but I couldn't find any relevant information. I hope you can help clarify this for me.