apply_evalue_cutoff: Filter the data by E-value

In evanamartin/TopPICR: What the Package Does (One Line, Title Case)

Filter the data by E-value

Description

The control_fdr() function filters the data by E-value for each annotation type. If the E-values from the eval_cutoff() function are used the overall FDR will fall below the given threshold.

Usage

apply_evalue_cutoff(x, e_vals)

Arguments

x

A data.table output from the augment_annotation function.

e_vals

A vector of three numeric values to be used as E-value cutoffs. The E-value cutoffs must be in the order of unique(x$AnnType). For example, if unique(x$AnnType) = "SwissProt", "TrEMBL", "VarSplic" then the E-value cutoff for SwissProt must be the first element of e_vals, the E-value cutoff for TrEMBL must be the second element of e_vals, and the E-value cutoff for VarSplic must be the third element of e_vals.

Value

A data.table with the rows removed that fall below the E-value cutoff.

Author(s)

Evan A Martin

evanamartin/TopPICR documentation built on Dec. 9, 2022, 8:05 p.m.