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I am attempting to reconstruct a function from R to Python that can differentiate between malignant and benign tumor cells recently, and it seems that the infercnvpy does not generate this output file as the R package.
In R, the function that I'm trying to reconstruct utilies a direct output file named infercnv.observations.txt, which is the tumor cell matrix data values. This file is automatically generated by running infercnv_obj <- infercnv::run(infercnv_obj, ...). In the R version of inferCNV, this generation of the file is determined by the parameter write_expr_matrix=T, which appears in the function plot_cnv that is written in the R script inferCNV_heatmap.R.
It could be seen from the code that this file is generated from the infercnv_obj@expr.data , then passed to obs_data in the function plot_cnv:
and is finally processed by the function heatmap.cnv that begins from line 1,373, before written into the txt file as follow:
if ("matrix" %in% is(obs_data)) {
if (write_expr_matrix) {
flog.info(paste("plot_cnv_observations:Writing observation data to", observation_file_base, sep=" "))
row.names(obs_data) <- orig_row_names
write.table(as.matrix(t(obs_data[data_observations$rowInd, data_observations$colInd])), file=observation_file_base)
}
}
As I am new to the python version of inferCNV, I am wondering does the infercnvpy contains the same data as the observations.txt after the analysis process is compelete? If it does exist, how could I extract it?
Thanks a lot for answering this question, it would really help me a lot with my study.
Sincerely yours.
The text was updated successfully, but these errors were encountered:
Description of feature
Hello,
I am attempting to reconstruct a function from R to Python that can differentiate between malignant and benign tumor cells recently, and it seems that the infercnvpy does not generate this output file as the R package.
In R, the function that I'm trying to reconstruct utilies a direct output file named infercnv.observations.txt, which is the tumor cell matrix data values. This file is automatically generated by running infercnv_obj <- infercnv::run(infercnv_obj, ...). In the R version of inferCNV, this generation of the file is determined by the parameter write_expr_matrix=T, which appears in the function plot_cnv that is written in the R script inferCNV_heatmap.R.
It could be seen from the code that this file is generated from the infercnv_obj@expr.data , then passed to obs_data in the function plot_cnv:
obs_data <- infercnv_obj@expr.data
and is finally processed by the function heatmap.cnv that begins from line 1,373, before written into the txt file as follow:
As I am new to the python version of inferCNV, I am wondering does the infercnvpy contains the same data as the observations.txt after the analysis process is compelete? If it does exist, how could I extract it?
Thanks a lot for answering this question, it would really help me a lot with my study.
Sincerely yours.
The text was updated successfully, but these errors were encountered: