Pooled analysis of radiation hybrids to identify genes for cell growth and paclitaxel action

SUMMARY

Data from bulk segregant analysis of radiation hybrids to identify genes for cell growth and paclitaxel action.

LaTeX DOCUMENTS

The 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 documents can be found by search. The pdf output file of the latex documents is "master.pdf".

SCRIPTS

The scripts necessary to analyze the data are in the "Data_Figs" directory and can also be found by search. The vast majority of the data files needed to run the scripts are in the directory "RH_pools_workspace_1". A few miscellaneous data files are in the "Data_Figs" directory.

FINDING RELEVANT SCRIPTS

For example, the second paragraph in the "Results" section ("master.pdf") commences with the phrase "We created six independent RH pools...", and provides some basic statistics on the RH pools. Searching for this phrase in "main.tex" reveals the names of two R scripts "clone_sem_1.R" and "graph_Human_retent_2.R" above the paragraph. These scripts provide the corresponding results.

Inspection of the script "clone_sem_1.R" shows that it uses the data file "clone.txt", while the script "graph_Human_retent_2.R" uses the data files "RH_pool_human_total_align.txt", "RH_pool_hamster_total_align.txt", "RH_human_gseq.txt", "RH_hamster_gseq.txt", "gencode_gtf_ensembl_ucsc_v31.txt", "clone.txt" and "cell_label_info.txt". All these data files can be found in the directory "RH_pools_workspace_1".

FINDING RELEVANT PARTS OF SCRIPTS

Statistics in the LaTeX documents have been quoted to unrealistic levels of precision, but are rounded in the pdf output file, "master.pdf". However, the redundant digits can be useful. For example, in the last paragraph on pg S12 of the "Supporting Information" (section "Overlap of interaction loci with growth and paclitaxel loci"), we are informed that "There were 15 genes that overlapped between the interaction loci and the 859 unique growth loci (odds ratio = 22.6, P = 8.3 × 10−15, Fisher’s Exact Test)..."

Reference to "supp.tex" reveals that the pertinent script is "g_d_comb_fish_2.R" and that the exact P value is "8.281682e-15". Searching "g_d_comb_fish_2.R" for "8.281682e-15" takes the reader to the relevant part of the script.