No Evidence for Sex-Differential Transcriptomes Driving Genome-Wide Sex-Differential Natural Selection

Matthew J. Ming, Changde Cheng, Mark Kirkpatrick, Arbel Harpak

Here are the code and scripts used to produce the analysis for "No Evidence for Sex-Differential Transcriptomes Driving Genome-Wide Sex-Differential Natural Selection"

Overview:

1. All code can be found in the main directory. There are no subdirectories
2. The following software were used:
   • R
   • RStudio
   • bcftools
3. The following R packages were used:
   • library(ggplot2)
   • library(ggpubr)
   • library(vroom)
   • library(ggrepel)
   • library(grid)
   • library(pBrackets)

Script documentation

Main code is contained in R scripts. The Slurm script listed as script 2 is a wrapper which run R code over multiple files (e.g., multiple ancestries or tissue types). The slurm file is listed with a number (2) and the R scripts run by this slurm file is listed as number and letter (2a). Scripts 3 and 4 each have 2 versions, one for all non-gonad tissues and one for gonads. The gonad version is listed as 3a and 4a respectively.

All final figures were produced using TwinPeaksFigs_Rev_FINAL.R.

1.ChengRepTwinPeaks_Anc.R

Get original Twin Peaks curve from 1000 Genomes data (Fig 2)

2. ChengRepRand_GTExONLY.slurm

Get Twin Peaks curves from sex label randomization in GTEx over multiple iterations (Fig 2)

2a. ChengRepTwinPeaks_Rand_GTEx.R

R script called by ChengRepRand_GTExONLY.slurm for getting Twin Peaks sex label randomization (Fig 2)

3. NewAnalysis_eQTLRegression_MH.R

Get A-values for updated linear regression method analysis in all tissues (except gonads) (Fig S1)

3a. NewAnalysis_eQTLRegression_MH_Gonads.R

Same as NewAnalysis_eQTLRegression_MH.R, but modified slightly for the gonads specifically (Fig S1)

4. NewAnalysis_eQTLRegression_MH_Revision.R

Get A-values using an improved weighted Standard Major Axis regression method (Fig 3)

4a. NewAnalysis_eQTLRegression_MH_Gonads_Revision.R

Same as NewAnalysis_eQTLRegression_MH_Revision.R, but modified slightly for the gonads specifically (Fig 3)

5. TwinPeaksFigs_Rev_FINAL.R

Final script for composing both main text and supplemental figures (Figs 1-3, S1). Depends on output from all previous scripts