This package contains both datasets and scripts (R) supporting the manuscript of MRI-informed muscle biopsies correlate MRI with pathology and DUX4 target gene expression in FSHD. The shell script /scripts/do_tophat.sh
performed the preprocessing and /scripts/*.R
the analysis for the manuscript. See more detail in /scripts/ReadMe.txt
.
List below are the major datasets and scripts that were used for the analysis. Note that the scripts for data exploratory are also included in the scripts folder, and so they might be a bit messy.
|- data |- se.rda: `RangedSummarizedExperiment` instance as a container containing gene counts, gene annotation and metadata. |- sanitized.dds.rda: sanitied/filtered `DESeqDataSet` of `se`, containing dispersion estimation and size factor, used for downstream analysis |- sanitized.rlg.rda: sanitized/filtered rlog-transformed dataset of sanitized.dds, used to visualize sample space |- scripts |- *.Rmd: R markdown document and notebook |- makeSE.R: get gene count and make a `RangedSummarizedExperiment` instance |- rankScore.R: get DUX4 rank and scores |- makeManuscripts_scatterPlot.R: make Figure 1
makeSE.R -> rankScore.R -> makeManuscripts_scatterPlot.R -> Figure 1
- R (3.5): pheatmap, xlsx, ggplot2, gridExtra
- Bioconductor (3.7)
- DESeqs (differential analysis)
- goseq (GO analysis)
- GenomicAlignments (gene counts)
- org.Hs.eg.db (annotation)
- GO.db (GO annotation)
- Optional (Customized pakcages for gene counts)
- hg38.HomoSapiens.Gencode.v24 (standard TxDb package built from gencode GFF v24)