Hey Dongjun,
Sorry to bother you again, but I have run into some new issues. I successfully merged everything, and was able to construct and read the bin-level data for all fields (chip, input, M, GC, N). When I attempted to run:
> mosaicsFit(bin1, analysisType = "TS", parallel=TRUE, nCore=10)
I received the following output:
Use 'parallel' package for parallel computing.
Info: background estimation method is determined based on data.
Info: background estimation based on bins with low tag counts.
Info: two-sample analysis (with mappability & GC content).
Info: use adaptive griding.
Info: fitting background model...
Info: grid = 0.01
Info: grid = 0.02
Info: grid = 0.04
Info: grid = 0.1
Info: grid = 0.2
Info: grid = 0.5
Info: done!
Info: fitting one-signal-component model...
RCPP_FUNCTION_5 is deprecated, it will be removed permanently in july
2014
Error in while (abs(logLik[iter] - logLik[iter - 1]) > eps & iter < 10) { :
missing value where TRUE/FALSE needed
Here is my entire R script
require(parallel)
library("mosaics")
bin1 <- readBins(type = c("chip", "input", "M", "GC", "N"), fileName =
c("chip.sam_fragL200_bin50.txt", "input.sam_fragL200_bin50.txt",
"hg19_ebv_M_fragL200_bin50.txt", "hg19_ebv_GC_fragL200_bin50.txt",
"hg19_ebv_N_fragL200_bin50.txt"),parallel=FALSE, nCore=8)
Info: reading and preprocessing bin-level data...
Info: assume that data contains more than one chromosome
Info: done!
------------------------------------------------------------
Info: preprocessing summary
------------------------------------------------------------
[Note] Bins with ambiguous sequences will be excluded from the analysis.
Coordinates before & after preprocessing:
chr1: 0 - 249240750 -> 9800 - 249240750
chr10: 0 - 135524850 -> 59800 - 135524850
chr11: 0 - 134946650 -> 59800 - 134946650
##
## Rest of Chromosomes
##
chrX: 0 - 155260600 -> 59800 - 155260600
chrY: 0 - 59363600 -> 9800 - 59363600
------------------------------------------------------------
> bin1
Summary: bin-level data (class: BinData)
----------------------------------------
- # of chromosomes in the data: 94
- total effective tag counts: 53211162
(sum of ChIP tag counts of all bins)
- control sample is incorporated
- mappability score is incorporated
- GC content score is incorporated
- uni-reads are assumed
----------------------------------------
chrID: # of bins, total effective tag counts
chr1: 4505951, 4460158
chr10: 2626437, 2599939
chr11: 2622660, 2390072
##
## Rest of Chromosomes
##
chr9_gl000199_random: 3394, 26182
chr9_gl000200_random: 3731, 0
chrY: 513221, 100143
----------------------------------------
> fit1 <- mosaicsFit(bin1, analysisType = "TS", parallel=TRUE, nCore=10)
Use 'parallel' package for parallel computing.
Info: background estimation method is determined based on data.
Info: background estimation based on bins with low tag counts.
Info: two-sample analysis (with mappability & GC content).
Info: use adaptive griding.
Info: fitting background model...
Info: grid = 0.01
Info: grid = 0.02
Info: grid = 0.04
Info: grid = 0.1
Info: grid = 0.2
Info: grid = 0.5
Info: done!
Info: fitting one-signal-component model...
RCPP_FUNCTION_5 is deprecated, it will be removed permanently in july
2014
Error in while (abs(logLik[iter] - logLik[iter - 1]) > eps & iter < 10) { :
missing value where TRUE/FALSE needed
Any ideas?