This function returns the indices in rds_gene_info for genes of interest. For instance, if we are interested in information about TP-53, we get the index of TP-53 in rds_gene_info. The current implementation assumes that rds_gene_info does not contain duplicates. If it happens that there are duplicates, it returns the index of the first occurrence. I think it should not be a problem in practice, but the following code extracts an rds_gene_info where there are indeed duplicates. If it's indeed not a problem feel free to close the issue.
my_friend = NetSciDataCompanion::CreateNetSciDataCompanionObject()
human_projects <- available_projects()
proj_info <- subset(
human_projects,
project == "SRP009615" & project_type == "data_sources"
)
expr <- create_rse(proj_info)
gene_info <- my_friend$extractSampleAndGeneInfo(expr)$rds_gene_info
https://github.com/QuackenbushLab/NetSciDataCompanion/blob/27e5c11cfc2e1802d7c22bdebc1d623cce9047a2/R/NetSciDataCompanion.R#L721
This function returns the indices in rds_gene_info for genes of interest. For instance, if we are interested in information about TP-53, we get the index of TP-53 in rds_gene_info. The current implementation assumes that rds_gene_info does not contain duplicates. If it happens that there are duplicates, it returns the index of the first occurrence. I think it should not be a problem in practice, but the following code extracts an rds_gene_info where there are indeed duplicates. If it's indeed not a problem feel free to close the issue.
my_friend = NetSciDataCompanion::CreateNetSciDataCompanionObject()
human_projects <- available_projects()
proj_info <- subset(
human_projects,
project == "SRP009615" & project_type == "data_sources"
)
expr <- create_rse(proj_info)
gene_info <- my_friend$extractSampleAndGeneInfo(expr)$rds_gene_info
https://github.com/QuackenbushLab/NetSciDataCompanion/blob/27e5c11cfc2e1802d7c22bdebc1d623cce9047a2/R/NetSciDataCompanion.R#L721