te.table {ORFik} | R Documentation

## Create a TE table

### Description

Creates a data.table with 6 columns, column names are:
variable, rfp_log2, rna_log2, rna_log10, TE_log2, id

### Usage

    te.table(df.rfp, df.rna, filter.rfp = 1, filter.rna = 1, collapse = FALSE)

### Arguments

`df.rfp` | a `experiment` of usually Ribo-seq or 80S from TCP-seq. (the numerator of the experiment, usually having a primary role)
`df.rna` | a `experiment` of usually RNA-seq. (the denominator of the experiment, usually having a normalizing function)
`filter.rfp` | numeric, default 1. What is the minimum fpkm value?
`filter.rna` | numeric, default 1. What is the minimum fpkm value?
`collapse` | a logical/character (default FALSE), if TRUE all samples within the group SAMPLE will be collapsed to one. If "all", all groups will be merged into 1 column called merged_all. Collapse is defined as rowSum(elements_per_group) / ncol(elements_per_group)

### Value

a data.table with 6 columns

### See Also

Other DifferentialExpression: `DEG.plot.static()`, `DTEG.analysis()`, `DTEG.plot()`, `te_rna.plot()`

### Examples

    df <- ORFik.template.experiment()
    df.rfp <- df[df$libtype == "RFP",]
    df.rna <- df[df$libtype == "RNA",]
    #te.table(df.rfp, df.rna)

[Package ORFik version 1.14.7 Index]