Description Usage Arguments Value Author(s) See Also Examples
View source: R/results_topTable.R
Calculate results
1 2 3 | 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 |
topTable of only the significant results
Complete topTable
Simon J Pelletier
topTable
,
MArrayLM
,
transcript_count
,
expr.toBind
1 2 3 4 5 6 7 | 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]]
|
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