auto_ge_analyzer: Auto Gene Expression Analysis
In xuzhougeng/zgtools: Xu Zhougeng's Toolkits

Description Usage Arguments Value Author(s)

View source: R/auto_ge_analyzer.R

Auto Gene Expression Analysis

auto_ge_analyzer(proj, filepath, type, colData, design, txDb, orgDb,
  keyType = "GENEID", column = "TXNAME", lfcThreashold = 0,
  pAdjustMethod = "BH", pThreshold = 0.05, goOnt = "MF",
  goKeytype = "TAIR", keggOrg = "ath", keggKeytype = "kegg", ...)

`proj`	project name
`filepath`	a `vector` of file path of gene count
`type`	method to count gene, one of HTSeq, Salmon, Sailfish, kallisto
`colData`	a `data.frame` containning sample information with columns of sample name, treatment
`design`	a `formula` which expresses how the counts for each gene depend on the variables in `colData`. Many R `formula` are valid, e.g, ~ group, ~ group + condition, ~genotype + treatment + genotype: treatment.
`txDb`	a `GenomicFeatures` object, which could be downloaded from `AnnotationHub`.
`orgDb`	orgDb, will be used for GO enrichment analysis
`lfcThreashold`	a non-negative value which specifies a log2 fold change threshold.
`pAdjustMethod`	the method to use for adjusting p-values, see ?p.adjust
`pThreshold`	a numeric to subset results of DESeq by pajust, default is 0.1
`goOnt`	one of "MF", "BP", and "CC" subontologies. BP: biological process CC: cellular component MF: molecular function
`goKeytype`	GO keytype
`keggOrg`	KEGG orgnism
`keggKeytype`	KEGG keytype
`...`	additional parameter