README.md

In machalen/AnalysisFunctions: Package with basic analysis functions for genomic data

AnalysisFunctions

Package with basic analysis functions for genomic data.

• createTargets: Function to create phenodata of the samples in the gene expression matrix.
• DeleteCtrlsGral: Function to delete control probe IDs from the expression matrix.
• gct.data4Tyers: Function to create gct format files for GSEA analysis.
• generate_cls: Function to create .cls format files for GSEA analysis.
• generate_gct: Function to create .gct format files for GSEA analysis.
• generate_rnk: Function to create .rnk files for GSEA analysis.
• MaxMin.Sym.Row: Function to resolve GeneID duplicates chosing the minimum or maximum values.
• Unique.Sym.Estimates: Function to resolve GeneID duplicates computing the mean and the median.
• data4TyersMake: Function to make a data frame with a structure of data4Tyers from arrays (RMA data).
• RNAseq.data4Tyers: Function to make a data frame with a structure of data4Tyers from RNAseq data.
• Complete.Human.GO.nd.KEGG: Function to complete annotations from RNAseq (featurecounts function) with GO and KEGG databases, for each gene and human specie.
• Complete.Mouse.GO.nd.KEGG: Function to complete annotations from RNAseq (featurecounts function) with GO and KEGG databases, for each gene and mouse specie.
• GSEA_report_HS: Function to make the report of GSEA based on human symbols
• GSEA_report_MS: Function to make the report of GSEA based on mouse symbols
• GSEA_report_ENSEMBL: Function to make the report of GSEA based on ENSEMBL IDs
• GSEA_genes_Report: Function to make the report of GSEA sumarized by gene

machalen/AnalysisFunctions documentation built on Nov. 11, 2019, 10:26 a.m.