summarize_cases: summarize_cases

In mskilab/casereport: casereport: Whole-genome + transcription based report for cancer genomes

summarize_cases

Description

Very ad-hoc function for mskilab use only!

takes a case report flow module and produces a data.table with links to the reports this is assuming that the reports are somewhere under /gpfs/commons/projects/imielinski_web

Usage

summarize_cases(
  jb,
  output_file = NULL,
  libdir = "~/git/casereport",
  html_dir = NULL,
  metadata = NULL
)

Arguments

jb	Flow Job object or a data.frame/data.table containing the contents of outputs(jb), where jb is the case report Flow Job object.
output_file	output TXT in which the tabular data will be saved. If not file is provided then the data is saved to a temporary file.
libdir	path to the casereport repository clone
html_dir	path to the directory in which to put the html version of the table
metadata	data.frame or data.table with additional metadata for the samples in jb. The metadata table must contain a header. The first column of the metadata should contain sample names that match the sample names in the Job object and should only contain unique values, otherwise this table is ignored and no metadata is added.

Value

data.table

mskilab/casereport documentation built on Oct. 19, 2022, 3 a.m.