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The molecular structure files are read from a user specified source directory.
Data read from standard input and the input files are read into numerous global variables that are referenced by multiple functions in the package.
The Excel files are read with JExcelApi.
Microarray files are read in R using BioConductor.
Care is taken to ensure that the files are read no more than once and the information that is often referred to is stored in the memory early on during runtime.
However, the main difference in the way i-Tracker handles these files is that.dta files, which represent a single spectrum, are read into memory before processing whilst.mgf files are read in to memory spectrum by spectrum whilst keeping the input file open.
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These files are reads all uploaded from August 9 10, 2006 (ti's range from 1397334945 – 1399236113) to for a total of 80,000 sequencing reads.
Raw data scans (.CEL files) were read into the R language and environment for statistical computing (version 2.15.1; R Foundation for Statistical Computing, Vienna, Austria; http://www.R-project.org/).org/
The CEL files were read in and spatially corrected using scripts from Borevitz et al. [3].
GPR files were read into the Bioconductor package LIMMA for further analysis in R [51], [52].
The raw data from CEL files were read into R.
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