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

In ptm: Analyses of Protein Post-Translational Modifications

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.

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.

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.

Author(s)

Juan Carlos Aledo

References

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

See Also

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

Examples

pos = env.matrices(hmeto$positive)[[2]][,-11]; ctr = env.matrices(hmeto$control)[[2]][,-11]
env.Ztest(pos, ctr, alpha = 0.0001)

ptm documentation built on Aug. 7, 2022, 5:05 p.m.