add_seed: add_seed

In scsR: SiRNA correction for seed mediated off-target effect

Description

This method takes in input a dataframe containing the results of an siRNA screen. This screen must contain the siRNA sequences in a dedicated column (the sequences have to be provided in the guide/antisense orientation). Then it adds a column with the seed of the siRNA sequences.

Usage

add_seed(df, seqColName="siRNA_seq", seedLength=7, startPosition=2)

Arguments

df	Dataframe containing the results of the siRNA screen.
seqColName	character vector with the name of the column that contains the siRNA sequences (the sequences have to be provided in the guide/antisense orientation).
seedLength	length of the seed in nucleotides (by default 7 bases) (integer)
startPosition	position in the siRNA sequence where the seed starts (by default position 2) (integer))

Value

screen data frame with the seed column added.

Author(s)

Andrea Franceschini

Examples

 data(uuk_screen)
 seed_uuk_screen = add_seed(uuk_screen[1:100,])

scsR documentation built on April 28, 2020, 7:11 p.m.