Man pages for syyang93/analyzeR
This package contains functions that Stephanie uses for her analysis of recount RNAseq data.
| examine_symbol | Gets the adjusted variable plot for mtDNA vs transcripts for... |
| examine_symbol.mesa | Gets the adjusted variable plot for mtDNA vs transcripts for... |
| examine_transcript | Gets the adjusted variable plot for mtDNA vs transcripts for... |
| filtering_steps | Filters out people who had incomplete RNAseq downloads from... |
| find_outliers | Finds PCA outliers - greater than 4 SD from the mean of the... |
| get_transcripts | Gets the transcripts for people who remain after filtering |
| get.vars | Function that will get the variables you need to run all the... |
| identify_pca_outliers | Filters transcripts based on expression levels. Also filters... |
| inv.norm.transform | Code for an inverse normal transformation, from Ryan |
| lm_test | Function that will allow for (apply) to be used for linear... |
| look_pca | Performs PCA, and tells you what percent of the variance each... |
| make.forestplot | Makes forestplots for genes of interest across tissues |
| make.subjids | Function that will return GTEx subject IDs when given sample... |
| perform.t.tests | Will perform t-tests and return pvals, confints, and... |
| perm.for.cutoff | Function that permutes the dataset and finds an appropriate... |
| perm.for.cutoff2 | Function that permutes the dataset and finds an appropriate... |
| perm.for.cutoff.transcripts | Function that permutes the dataset and finds an appropriate... |
| pval_qqplot | Function for drawing a p-value qqplot |
| remove_incomplete_covariates | Filter out individuals with incomplete phenotypes Phenotypes... |
| remove_mito_outlier | Remove individuals that are outliers in corrected mito... |
| run.all.lms | Function that will run a regression for your variable of... |
| run_lm | A wrapper for deciding either to run a default lm or a... |
| run_lm_default | Basic function that is used in run.all.lms. Needs to be... |
| testing_assoc | Function that tests for associations and returns results.... |
| testing_assoc.transcript | Function that tests for associations and returns results... |
