scsR (version 1.8.0)

create_sd_matrix: create_sd_matrix

Description

We observed that the standard deviation of the oligos that share the same seed do change relative to their average score. In principle we could plot this information on a graph (x-axis = average of the oligos that share the same seed, y-axes = standard deviation of the oligos). We do provide this utility method to condense this information in a matrix (that reports the quantiles of the standard deviation for every score interval).

Usage

create_sd_matrix(screen, seedColName="seed7", scoreColName="score")

Arguments

screen

data frame containing the results of the siRNA experiment.

seedColName

name of the column that contains the seeds sequences of the screen (character vector)

scoreColName

name of the column that contains the score of the screen (character vector)

Value

matrix that reports the quantiles of the standard deviation for every score interval.

Examples

	data(uuk_screen)
	
	
	# to speed up the example we use only the first 100 rows
	uuk_screen_reduced = uuk_screen[1:100,]

	screen = add_seed(uuk_screen_reduced)
	sd_matrix = create_sd_matrix(screen)