results_topTable: Calculate results
In spell098/rnaseq_app:

Description Usage Arguments Value Author(s) See Also Examples

Calculate results

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results_topTable(lm2.contrast, expr.toBind, pvalue = 0.05, logFC = 1,
  typeID = "ensembl_gene_id", genes_annotation_unique, annotations,
  adjust = "no")

`lm2.contrast`	MArrayLM object
`expr.toBind`	Expression data.matrix with supplemental colums: module and ID
`pvalue`	p-value limit (alpha)
`logFC`	log2 fold change limit #VERIFY IT IS REALLY LOG2 (default = 1)
`typeID`	The type of ID used (default="ensembl_gene_id")
`genes_annotation_unique`	All the annotations for every ID in the 2nd row in expr.toBind (or rownames of expr.matrix)
`annotations`	Annotation (???)
`adjust`	Which correction for multiple analysis to use (default = "no"). Note: None is different than no somehow

results: topTable of only the significant results
topTable3: Complete topTable

Simon J Pelletier

topTable , MArrayLM , transcript_count , expr.toBind

expr.matrix <- readRDS("data/expr_matrix_LGVD.rds")
design <- design_contrasts(get_names(colnames(expr.matrix)))
results_list <- results_topTable()
lm2 <- lm2Contrast(expr.matrix,design)
lm2.contrast = lm2[[1]]
contrasts=lm2[[2]]
contrast.matrix=lm2[[3]]