improve sample size estimation

[wolski]

https://www.statmethods.net/stats/power.html

[cpanse]

System Call

bfabric@fgcz-r-028

example call

Rscript <code.R> <yaml> <scratch> <input> <output>

/usr/bin/Rscript \
/path/to/script/code.R \
/scratch/SAMPLESIZEQC_256/WU199860//WU199860.yaml \
/scratch/SAMPLESIZEQC_256/WU199860/ \
/scratch/SAMPLESIZEQC_256/WU199860/1172863.zip \
/scratch/SAMPLESIZEQC_256/WU199860//output.pdf

YAML file

WU199860.yaml

application:
  input:
    MaxQuant:
    - bfabric@fgcz-ms.uzh.ch://srv/www/htdocs///p3000/bfabric/Proteomics/MaxQuant/2019/2019-03/2019-03-23/workunit_195062/1172863.zip
  output:
  - bfabric@fgcz-ms.uzh.ch:/srv/www/htdocs//p3000/bfabric/Proteomics/sample_size_qc/2019/2019-06/2019-06-06//workunit_199860//1284632.pdf
  parameters: {}
  protocol: scp
job_configuration:
  executable: /home/bfabric/sgeworker/bin/fgcz_sge_fgcz_sge_sample_size_qc.bash
  external_job_id: !!python/long '68718'
  input:
    MaxQuant:
    - resource_id: 1172863
      resource_url: https://fgcz-bfabric.uzh.ch/bfabric/userlab/show-resource.html?resourceId=1172863
  output:
    protocol: scp
    resource_id: 1284632
    ssh_args: -o StrictHostKeyChecking=no -2 -l bfabric -x
  stderr:
    protocol: file
    resource_id: 1284633
    url: /home/bfabric/sgeworker/logs/workunitid-199860_resourceid-1284632.err
  stdout:
    protocol: file
    resource_id: 1284634
    url: /home/bfabric/sgeworker/logs/workunitid-199860_resourceid-1284632.out
  workunit_id: 199860
  workunit_url: https://fgcz-bfabric.uzh.ch/bfabric/userlab/show-workunit.html?workunitId=199860

[wolski]

There is a sample size estimation application now available.