Load bcbio run

We recommend loading the bcbio-nextgen run as a remote connection over sshfs. This requires setting parent_dir in the function.

load_bcbio_run(template, organism, intgroup = NULL, parent_dir = getwd(),
  config_dir = NULL, final_dir = NULL)

Arguments

template

Template name (YAML filename, without the extension) originally called by bcbio_nextgen.py

organism

Organism (e.g. hsapiens)

intgroup

Interesting groups. Defaults to description if not set. First entry is used for plot colors during quality control analysis. Entire vector is used for PCA and heatmap QC functions.

parent_dir

Parent directory containing the run folder

config_dir

Set the config output directory, if non-standard

final_dir

Set the final output directory, if non-standard

Value

bcbio list object with directory paths

Examples

## Not run: ------------------------------------
# load_bcbio_run("illumina_rnaseq")
## ---------------------------------------------