Transcription Factor High Accumulation Zones

Documentation for package ‘TFHAZ’ version 1.29.0

accumulation	Creates a vector with accumulation counts of transcription factors for each chromosome base.
base_dense_w_10	Contains an output of the dense_zones function.
dense_zones	Finds transcription factor dense DNA zones for different accumulation threshold values.
high_accumulation_zones	Finds transcription factor high accumulation DNA zones.
Ishikawa	Contains genomic regions of transcription factors at the ranges side and the name of the transcription factors at the metadata side.
n_zones_PCA	Principal Component Analysis of the number of dense zones obtained with the three methods of accumulation (TF, region, base).
plot_accumulation	Plots the accumulation vector obtained with the accumulation function.
plot_n_zones	Plots the number of dense zones for each threshold value.
reg_dense_w_10	Contains an output of the dense_zones function.
TF_acc_w_0	Contains an output of the accumulation function.
TF_dense_w_0	Contains an output of the dense_zones function.
TF_dense_w_10	Contains an output of the dense_zones function.
TF_dense_w_100	Contains an output of the dense_zones function.
TF_dense_w_1000	Contains an output of the dense_zones function.
TF_dense_w_10000	Contains an output of the dense_zones function.
w_analysis	Shows the number of dense zones obtained with different values of base neighborhood window width.