ptm (version 0.2.2)

env.Ztest: Preferred/Avoided Amino Acids Within an Environment

Description

Searches for amino acids either overrepresented or avoided at given positions within a sequence environment.

Usage

env.Ztest(pos, ctr, alpha = 0.05)

Arguments

pos

a 21 x m matrix containing the absolute frequencies of 21 amino acids at the m positions, in the positive environments.

ctr

a 21 x m matrix containing the absolute frequencies of 21 amino acids at the m positions, in the control environments.

alpha

significance level.

Value

Returns a list with three elements: (1) a matrix with the values of the Z statistical. (2) A dataframe with information regarding amino acid overrepresented in the positive environments, and (3) a dataframe similar to the previous one, but for amino acids avoided from the positive environments.

Details

Please, note that in addition to the 20 proteinogenetic amino acid we are using the symbol X when the target (central) residue is closer to the N-terminal or C-terminal of the protein than the radius used.

References

Aledo et al. Sci Rep. 2015; 5: 16955. (PMID: 26597773)

See Also

env.extract(), env.matrices() and env.plot()

Examples

# NOT RUN {
pos = env.matrices(hmeto$positive)[[2]][,-11]; ctr = env.matrices(hmeto$control)[[2]][,-11]
env.Ztest(pos, ctr, alpha = 0.0001)
# }