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gmelloni / PrecisionTrialDrawer

A set of tools to help bioinformaticians, clinicians and biostatisticians to design, analyze and finalize a custom gene panel for clinical trial in cancer genomics.
GNU General Public License v3.0
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CNA only panel Error #1

Closed alessando-guida closed 6 years ago

alessando-guida commented 6 years ago

When submitting a dataframe as follows

library(PrecisionTrialDesigner)
library(kable)

genes = c("BRCA1", "BRCA2")

panel_design <- data.frame(drug = ""
                         , gene_symbol = genes
                         , alteration = "CNA"
                         , exact_alteration = "amplification"
                         , mutation_specification = ""
                         , group = ""
)

which returns the following table

kable(panel_design)
drug gene_symbol alteration exact_alteration mutation_specification group
BRCA1 CNA amplification
BRCA2 CNA amplification 
#DESIGN
panel <- newCancerPanel(panel_design)
#DOWNLOAD alternative
panel <- getAlterations(panel, tumor_type="brca")

The following error is reported

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 2 did not have 6 elements

gmelloni commented 6 years ago

I ran the example but I can't reproduce the error 🤔 I am working on the latest R 3.5 on MacOS

alessando-guida commented 6 years ago

bug now fixed