te.table: Create a TE table

In Roleren/ORFik: Open Reading Frames in Genomics

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(), DEG_model(), 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)

Roleren/ORFik documentation built on April 25, 2024, 8:41 p.m.