create_processed_report {scPipe} | R Documentation |
create an HTML report summarising pro-processed data. This is an alternative to the more verbose create_report
that requires only the processed counts and stats folders.
create_processed_report(outdir = ".", organism, gene_id_type, report_name = "report")
outdir |
output folder |
organism |
the organism of the data. List of possible names can be retrieved using the function 'listDatasets'from 'biomaRt' package. (i.e 'mmusculus_gene_ensembl' or 'hsapiens_gene_ensembl') |
gene_id_type |
gene id type of the data A possible list of ids can be retrieved using the function 'listAttributes' from 'biomaRt' package. the commonly used id types are 'external_gene_name', 'ensembl_gene_id' or 'entrezgene' |
report_name |
the name of the report .Rmd and .html files. |
## Not run: create_report( outdir="output_dir_of_scPipe", organism="mmusculus_gene_ensembl", gene_id_type="ensembl_gene_id") ## End(Not run)