Description Usage Arguments See Also Examples
Extract a list (a character vector indeed) of genes from a topTable outputted by the limma software
1 2 3 | genesFromTopTable(aTopTable, filename = NULL, entrezOnly = TRUE,
uniqueIds = TRUE, adjOrrawP = "adj", Pcutoff = 0.05, FCcutoff = 1,
updown = "both", id2Select = "ENTREZ", cols2Select = 0)
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aTopTable |
A top table file such as produced by the limma package or the UEB pipeline |
filename |
Name of the file that contains the topTable (to be used if the topTable is not in memory yet) |
entrezOnly |
To decide if only lines with a meaningful entrez symbol should be retained. Defaults to TRUE. |
uniqueIds |
To decide if duplicate identifiers should be removed after the selection defined by other parameters. Defaults to TRUE. |
adjOrrawP |
To decide if filtering is based on raw or adjusted p-values. Defaults to 'adj'. |
Pcutoff |
The filtering cutoff for p-values (if these are raw or adjusted is set by 'adjorRaw' parameter). |
FCcutoff |
The filtering cutoff for fold change. |
updown |
To decide which values to retain : up-regulated (FoldC >0 ), downregulated (FoldC < 0) or both. Defaults to 'both'. |
id2Select |
To decide which identifiers are to be selected. Defaults to 'ENTREZ'. Possible values are: ("ENTREZ","SYMBOL", NULL) but the alias ("Entrez", "EntrezsA", "Symbols", "SymbolsA") are accepted. |
cols2Select |
To decide which (and how many) columns are to be selected. Set 'cols2Select' to a (single or vector) value if no preferred identifier is known. It is used ony when 'id2select' is set to NULL. This parameter is dangerous because if more than 2 columns are selected the output is not a character vector and cannot be used as such. |
limma
1 2 3 4 5 6 | fileName<- system.file("extdata", "ExpressAndTop_AvsB.csv2", package = "geneLists")
AvsB <- read.table(fileName, header=TRUE, sep=";", dec=",", row.names=1)
entrezs_01_up <- genesFromTopTable (AvsB, entrezOnly = TRUE, uniqueIds=TRUE, adjOrrawP = "adj", Pcutoff = 0.01, FCcutoff=1, updown="up", id2Select = "ENTREZ", cols2Select =0)
length(entrezs_01_up)
table_01_up <- genesFromTopTable (AvsB, entrezOnly = TRUE, uniqueIds=TRUE, adjOrrawP = "adj", Pcutoff = 0.01, FCcutoff=1, updown="up", id2Select = NULL, cols2Select =1:3)
dim(table_01_up)
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