REPTILE (version 1.0)

calculate_epimark_deviation: Internal - calculating intensity deviation feature

Description

Internal function used to calculate the intensity deviation features. It is based on the epigenomic signatures of a given region in target sample, where prediction will be generated, and reference samples. Intensity deviation is defined as the intensity in target sample subtracted by the mean intensity in reference samples (i.e. reference epigenome) and it captures the tissue-specificity of each epigenetic mark.

Usage

calculate_epimark_deviation(data_info, x, query_sample, ref_sample = NULL)

Arguments

data_info

data.frame instance generated by reading data information file specifying the samples and marks used in the analysis. The data.frame includes at least two columns named "sample" and "mark", corresponding to the samples and marks included.

x

data.frame instance generated by reading epimark file. The first four columns of the data.frame are "chr", "start", "end" and "id" of each region in the epimark file. The rest columns contain values of epigenetic marks in samples as specified in data_info and column names are under MARK_SAMPLE format, such as "H3K4me1_mESC".

query_sample

name of the target sample

ref_sample

a vector of names of the reference sample(s)

Value

data.frame instance containing intensity deviation values of each mark

See Also

read_epigenomic_data