a vector of integers, each elemetnt represents the number of reads from a binding site in the IP sample
INPUT
a vector of integers, each elements represents the number of reads from a binding site in the Input control sample
TOTAL_IP
an integer, which represents the total number of reads in IP sample
TOTAL_INPUT
an integer, which represents the total number of reads in Input control sample
FOLD
a decimal number, which indicates the ration of Possion mean to be tested, default: 1. Use a larger number for detection of highly enriched binding sites.
minimal_counts_in_fdr
an integer threshold, only the loci with reads more than this number are subjected for fdr calculation. default: 10
Value
The function returns a list of length 3, which contains the log(p-value), log(fdr) and log(fold change), respectively.
Details
c-test is used to compare two Poisson means, for peak calling or binding sites identification in exomePeak R-package. The comparison of two
Possion distributions is converted into a binomial distribution based test. The number of reads at the same locus for the aligned reads are
counted by other packages, such as Rsamtools or HTseq-count.
References
Przyborowski, J. and Wilenski, H. (1940) Homogeneity of results in testing samples from Poisson series: with an application to testing clover seed for dodder. Biometrika, 31, 313-323