Man pages for ahmedelmahy/RNASeqclassifier1
A collection of functions for feature selection and classifier development from RNASeq data.

class_predictCreate confusion matrix of the predictions vs reference class...
compare_selected_features_barplotplot the counts of the selected genes though samples colored...
deg_deseq2Select diffentially expressed genes(DGEs) from a DESeqDataSet...
deg_voomSelect diffentially expressed genes(DGEs) from a voom object
eliminate_glmEliminate features with glmnet
eliminate_RFEliminate features with Random forest by sorting variable...
filter0Basic filter which just removes very low expressed genes or...
filter_cpmfilter low expressed genes using cpm
filter_linear_correlationfilter genes by linear correlation with the class variable
filter_stepStepwise feature selection
fit_glmfit a glmnet model
fit_rffit a random forest model
fit_svmLinearfit a svmLinear
fit_svmRadialfit a svmRadial
get_classGet class vector from the rse_gene
load_datadownload an Rdata object from the recount2 project to be...
normalize_deseq2Normalize counts matrix with DESeq2
normalize_voomNormalize counts matrix with voom
pcaPlot top four principle components in a counts matrix colored...
plot_multipe_rocsplot ROC curves from all models
tidyClassClean a class vector by keeping only alphabetical letters to...
ahmedelmahy/RNASeqclassifier1 documentation built on May 16, 2018, 1:27 a.m.