Cost-effective mapping of genetic interactions in mammalian cells

LaTeX DOCUMENTSThe LaTeX documents "master.tex", "main.tex" and "supp.tex" are located in the "Words" directory and provide the key to navigate the scripts and data. These ".tex" documents can be found by search. The pdf output file of the latex documents is "master.pdf".
SCRIPTS AND DATAThe scripts necessary to analyze the data are in the various directories and can also be found by search. The vast majority of the data files needed to run the scripts are in the directory "data". A few miscellaneous data files are in the local "data" directory for each analysis. The file "RH_Ix_seq.txt" documents the RH-Seq genetic interactions and is also provided as a standalone file.
FINDING RELEVANT SCRIPTSFor example, the first paragraph in the "Results" ("master.pdf") includes the phrase "Fifteen independent RH clones...", and provides some basic statistics on sequencing depth. Searching for this phrase in "main.tex" reveals the names of three R scripts "Seq_reads_1.R", "Retent_1.R" and "RH_cnv_1.R" above the relevant paragraph. "Seq_reads_1.R" provides the corresponding results.
Inspection of the script "Seq_reads_1.R" shows that it uses the data file "hg38_chr_length_ucsc.txt", while the script "Retent_1.R" uses the data file "RH_1Mb.txt". Both these data files can be found in the directory "data". "Seq_reads_1.R" also uses "GENE_INT_mapped_reads_info.txt", which can be found in the "data" directory local to "Seq_reads_1.R", in the "Seq_reads" directory.
FINDING RELEVANT PARTS OF SCRIPTSStatistics in the LaTeX documents have been quoted to unrealistic levels of precision, and are rounded in the pdf output file, "master.pdf". Nevertheless, the redundant digits can be useful. For example, in the second paragraph of the "Results", we are informed that "The human DNA fragment length was 2.3 ± 0.1 Mb..."
Looking at "main.tex" reveals that the exact fragment length is "2.265945" Mb and that there are three R scripts corresponding to the paragraph. The relevant script is "RH_cnv_1.R" and searching "RH_cnv_1.R" for "2.265945" takes the reader to the relevant part of the script.