Wraps the iSeq R package that implements the methods described in "A fully Bayesian hidden Ising model for ChIPseq data analysis" by Qianxing Mo
Version  1.0 

Bundle  sequencing 
Categories  
Authors  Lauri Lyly (lauri.lyly@helsinki.fi) 
Issue tracker  View/Report issues 
Requires  iSeq (Rbioconductor) 
Source files  component.xml iSeq.r 
Usage  Example with default values 
Name  Type  Mandatory  Description 

treatment  CSV  Mandatory  Sample CSV file, with fields: chromosome name, region middle position, strand (either 1 for forward or 2 for reverse) 
control  CSV  Mandatory  Control CSV file with similar format as treatment file. 
Name  Type  Description 

peaks  CSV  Called peaks regions returned from peakreg: A data frame with rows corresponding to enriched regions and columns corresponding to the following: chr: Chromosome IDs. gstart: The start genomic position of the enriched region. gend: The end genomic position of the enriched region. rstart: The row number for gstart in chrpos. rend: The row number for gend in chrpos. peakpos: The inferred center (peak) of the enriched region. meanpp: The mean posterior probability of the merged regions/bins. ct1: total tag counts for the region from gstart to gend for the chain corresponding to count[,1]; ct1=sum(count[rstart:rend,1]) ct2: total tag counts for the region from gstart to gend for the chain corresponding to count[,1]; ct2=sum(count[rstart:rend,2]) ct12: ct12 = ct1 + ct2 sym: A parameter used to measure if the forward and reverse tag counts are symmetrical (or balanced) in enriched regions. The values range from 0.5 (perfect symmetry) to 0 (complete asymmetry). 
report  Latex  Various plots. To be determined more exactly  no plot is yet produced. 
Name  Type  Default  Description 

a0  float  1  a0: The scale hyperparameter of the Gamma prior, alpha0. 
a1  float  0.5  a1: The scale hyperparameter of the Gamma prior, alpha1. 
b0  float  1  b0: The rate hyperparameter of the Gamma prior, beta0. 
b1  float  1  b1: The rate hyperparameter of the Gamma prior, beta1. 
burnin  int  500  burnin: The number of MCMC burnin iterations. 
ctcut  float  0.95  ctcut: A value used to set the initial state for each window/bin. If tag count of a bin is greater than quantile(Y[,4],probs=ctcut), its state will be set to 1, otherwise 1. For typical ChIPseq data, because the major regions are nonenriched, a good value for ctcut could be in the interval (0.9, 0.99). 
cutoff  float  0.5  The cutoff value (a scalar) used to call enriched bins. If use posterior probability as a criterion (method="ppcut"), a bin is said to be enriched if its pp is greater than the cutoff. If use FDR as a criterion (method="fdrcut"), bins are said to be enriched if the binbased FDR is less than the cutoff. The FDR is calculated using a direct posterior probability approach (Newton et al., 2004). The default value 0.5 is applicable to ppcut, a more likely default for fdrcut would be 0.05. 
gap  int  300  gap: gap is the average length of the sequenced DNA fragments. If the distance between two nearest bins is greater than 'gap', a bin with 0 tag count is inserted into the two bins for modeling. 
k0  float  3  k0: The initial parameter used to control the strength of interaction between neighboring bins, which must be a positive value (k0>0). A larger value of kappa represents a stronger interaction between neighboring bins. 
maxgap  int  300  The criterion used to merge enriched bins. If the genomic distance of adjacent bins is less than maxgap, the bins will be merged into the same enriched region. 
maxk  float  10  Unused for iSeq2. maxk: The maximum value of k(kappa) allowed. 
maxlen  int  80  The maximum length of the genomic window/bin into which sequence tags are aggregated. 
method  string  "iSeq1"  Either iSeq1 or iSeq2. iSeq1 implements the method that models the binbased tag counts using PoissonGamma distribution and the hidden states of the bins using a standard 1D Ising model. iSeq2 is similar but uses a hidden highorder Ising model. 
mink  float  0  Unused for iSeq2. mink: The minimum value of k(kappa) allowed. 
minlen  int  10  The minimum length of the genomic window/bin into which sequence tags are aggregated. 
normsd  float  0.1  Unused for iSeq2. normsd: iSeq1 uses a Metropolis random walk proposal for sampling from the posterior distributions of the model parameter kappa. The proposal distribution is a normal distribution with mean 0 and standard deviation specified by normsd 
ntagcut  int  10  The tag count cutoff value for triggering bin size change. For example, suppose L_i and C_i are the length and tag count for bin i, respectively. If C_i >= ntagcut, the length for bin i+1 will be min(L_i/2,minlen); if C_i < ntagcut, the length for bin i+1 will be max(2*L_i, maxlen). Note, by default, the bin sizes decrease/increase by a factor of 2. Thus, the user should let maxlen = (2^n)*minlen. 
peakreg_method  string  "ppcut"  'ppcut' or 'fdrcut', depending on whether cutoff is applied to posterior probability values or false discovery rate. 
sampling  int  2000  sampling: The number of MCMC sampling iterations. The posterior probability of enriched and nonenriched state is calculated based on the samples generated in the sampling period. 
verbose  boolean  false  verbose: A logical variable. If TRUE, the number of completed MCMC iterations is reported. 
Test case  Parameters▼  IN treatment 
IN control 
OUT peaks 
OUT report 


case1  properties  treatment  control  (missing)  (missing)  
