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Using biocmanager for flowcore and biobase #3

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Using biocmanager for flowcore and biobase #3

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4409297
Added bioconductor and fix spelling
Aug 19, 2019
b4d9974
Revert "Added bioconductor and fix spelling"
Aug 19, 2019
5aa3a27
Using biocmanager to install flowcore and biobase
Aug 19, 2019
bad5b4c
Change the way files with csv/fcs extension are found
Aug 19, 2019
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12 changes: 8 additions & 4 deletions FCS-to-CSV v2.0.R
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Expand Up @@ -9,8 +9,12 @@
##### USER INPUT #####

# Install packages if required
if(!require('flowCore')) {install.packages('flowCore')}
if(!require('Biobase')) {install.packages('Biobase')}
# BiocManager is used to provide compatibility for flowCore for R version 3.6 and above.
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("flowCore")
BiocManager::install("Biobase")
Comment on lines +12 to +16
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As far as I can see, this change might break backwards-compatibility with older versions of R.

@tomashhurst Would you accept a pull request with an if statement that checks for the R version and then either uses the current code (R < 3.6) or the code @ghar1821 suggested for higher R versions?

Chris

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That certainly would! There might be some issues with the Bioconductor end of things, but we can certainly try that out.


if(!require('data.table')) {install.packages('data.table')}

# Load packages
Expand All @@ -31,8 +35,8 @@
#PrimaryDirectory <- getwd() # Assign the working directory as 'PrimaryDirectory'
#PrimaryDirectory

## Use to list the .csv files in the working directory -- important, the only CSV files in the directory should be the one desired for analysis. If more than one are found, only the first file will be used
FileNames <- list.files(path=PrimaryDirectory, pattern = ".fcs") # see a list of CSV files
## Use to list the .fcs files in the working directory -- important, the only FCS files in the directory should be the one desired for analysis. If more than one are found, only the first file will be used
FileNames <- list.files(path=PrimaryDirectory, pattern = ".fcs") # see a list of FCS files
as.matrix(FileNames) # See file names in a list

## Read data from Files into list of data frames
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