## ----eval=FALSE--------------------------------------------------------------- # library("FitHiC") # fragsfile <- system.file("extdata", "fragmentLists/Duan_yeast_EcoRI.gz", # package = "FitHiC") # intersfile <- system.file("extdata", "contactCounts/Duan_yeast_EcoRI.gz", # package = "FitHiC") # outdir <- file.path(getwd(), "Duan_yeast_EcoRI") # FitHiC(fragsfile, intersfile, outdir, libname="Duan_yeast_EcoRI", # distUpThres=250000, distLowThres=10000) ## ----run, echo=FALSE, collapse=TRUE, warning=FALSE---------------------------- library("FitHiC") fragsfile <- system.file("extdata", "fragmentLists/Duan_yeast_EcoRI.gz", package = "FitHiC") intersfile <- system.file("extdata", "contactCounts/Duan_yeast_EcoRI.gz", package = "FitHiC") outdir <- file.path(getwd(), "Duan_yeast_EcoRI") FitHiC(fragsfile, intersfile, outdir, libname="Duan_yeast_EcoRI", distUpThres=250000, distLowThres=10000) ## ----run-visual, echo=FALSE, message=FALSE, warning=FALSE, results="hide"----- library("FitHiC") fragsfile <- system.file("extdata", "fragmentLists/Duan_yeast_EcoRI.gz", package = "FitHiC") intersfile <- system.file("extdata", "contactCounts/Duan_yeast_EcoRI.gz", package = "FitHiC") outdir <- file.path(getwd(), "Duan_yeast_EcoRI") FitHiC(fragsfile, intersfile, outdir, libname="Duan_yeast_EcoRI", distUpThres=250000, distLowThres=10000, visual=TRUE) ## ----calculate-probabilities, echo=FALSE, results="asis"---------------------- output <- file.path(getwd(), "Duan_yeast_EcoRI", "Duan_yeast_EcoRI.fithic_pass1.txt") data <- read.table(output, header=TRUE) knitr::kable(head(data, n=6L), caption="Duan_yeast_EcoRI.fithic_pass1.txt") output <- file.path(getwd(), "Duan_yeast_EcoRI", "Duan_yeast_EcoRI.fithic_pass2.txt") data <- read.table(output, header=TRUE) knitr::kable(head(data, n=6L), caption="Duan_yeast_EcoRI.fithic_pass2.txt") ## ----fit-spline, echo=FALSE, results="asis"----------------------------------- output <- file.path(getwd(), "Duan_yeast_EcoRI", "Duan_yeast_EcoRI.spline_pass1.significances.txt.gz") data <- read.table(gzfile(output), header=TRUE) knitr::kable(head(data, n=6L), align="crcrrrr", caption="Duan_yeast_EcoRI.spline_pass1.significances.txt.gz") output <- file.path(getwd(), "Duan_yeast_EcoRI", "Duan_yeast_EcoRI.spline_pass2.significances.txt.gz") data <- read.table(gzfile(output), header=TRUE) knitr::kable(head(data, n=6L), align="crcrrrr", caption="Duan_yeast_EcoRI.spline_pass2.significances.txt.gz") ## ----echo=FALSE, message=FALSE, warning=FALSE, results="hide"----------------- fragsfile <- system.file("extdata", "fragmentLists/Duan_yeast_HindIII.gz", package = "FitHiC") intersfile <- system.file("extdata", "contactCounts/Duan_yeast_HindIII.gz", package = "FitHiC") outdir <- file.path(getwd(), "Duan_yeast_HindIII") FitHiC(fragsfile, intersfile, outdir, libname="Duan_yeast_HindIII", distUpThres=250000, distLowThres=10000) ## ----message=FALSE, warning=FALSE, results="hide"----------------------------- library("FitHiC") fragsfile <- system.file("extdata", "fragmentLists/Dixon_hESC_HindIII_hg18_w40000_chr1.gz", package = "FitHiC") intersfile <- system.file("extdata", "contactCounts/Dixon_hESC_HindIII_hg18_w40000_chr1.gz", package = "FitHiC") outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_w40000_chr1") FitHiC(fragsfile, intersfile, outdir, libname="Dixon_hESC_HindIII_hg18_w40000_chr1", noOfBins=50, distUpThres=5000000, distLowThres=50000, visual=TRUE) ## ----message=FALSE, warning=FALSE, results="hide"----------------------------- library("FitHiC") fragsfile <- system.file("extdata", "fragmentLists/Dixon_hESC_HindIII_hg18_combineFrags10_chr1.gz", package = "FitHiC") intersfile <- system.file("extdata", "contactCounts/Dixon_hESC_HindIII_hg18_combineFrags10_chr1.gz", package = "FitHiC") outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_combineFrags10_chr1") FitHiC(fragsfile, intersfile, outdir, libname="Dixon_hESC_HindIII_hg18_combineFrags10_chr1", noOfBins=200, distUpThres=5000000, distLowThres=50000, visual=TRUE) ## ----message=FALSE, warning=FALSE, results="hide"----------------------------- library("FitHiC") fragsfile <- system.file("extdata", "fragmentLists/Dixon_mESC_HindIII_mm9_combineFrags10_chr1.gz", package = "FitHiC") intersfile <- system.file("extdata", "contactCounts/Dixon_mESC_HindIII_mm9_combineFrags10_chr1.gz", package = "FitHiC") outdir <- file.path(getwd(), "Dixon_mESC_HindIII_mm9_combineFrags10_chr1") FitHiC(fragsfile, intersfile, outdir, libname="Dixon_mESC_HindIII_mm9_combineFrags10_chr1", noOfBins=200, distUpThres=5000000, distLowThres=50000, visual=TRUE) ## ----message=FALSE, warning=FALSE, results="hide"----------------------------- library("FitHiC") fragsfile <- system.file("extdata", "fragmentLists/Dixon_hESC_HindIII_hg18_w40000_chr1.gz", package = "FitHiC") intersfile <- system.file("extdata", "contactCounts/Dixon_hESC_HindIII_hg18_w40000_chr1.gz", package = "FitHiC") outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_w40000_chr1.afterICE") biasfile <- system.file("extdata", "biasPerLocus/Dixon_hESC_HindIII_hg18_w40000_chr1.gz", package = "FitHiC") FitHiC(fragsfile, intersfile, outdir, biasfile, libname="Dixon_hESC_HindIII_hg18_w40000_chr1", noOfBins=50, distUpThres=5000000, distLowThres=50000, visual=TRUE) ## ----message=FALSE, warning=FALSE, results="hide"----------------------------- library("FitHiC") fragsfile <- system.file("extdata", "fragmentLists/data_5000000_abs.bed.gz", package = "FitHiC") intersfile <- system.file("extdata", "contactCounts/data_5000000.matrix.gz", package = "FitHiC") biasfile <- system.file("extdata", "biasPerLocus/data_5000000_iced.matrix.biases.gz", package = "FitHiC") outdir <- file.path(getwd(), "data_5000000") FitHiC(fragsfile, intersfile, outdir, biasfile, libname="data_5000000", distUpThres=500000000, distLowThres=5000000, visual=TRUE, useHiCPro=TRUE) ## ----fragsfile, echo = FALSE, results = "asis"-------------------------------- fragsfile <- system.file("extdata", "fragmentLists/Dixon_hESC_HindIII_hg18_w40000_chr1.gz", package = "FitHiC") data <- read.table(gzfile(fragsfile), header=FALSE, col.names=c("Chromosome Name", "Column 2", "Mid Point", "Hit Count", "Column 5")) knitr::kable(head(data, n=6L), align = "crrrr", caption="FRAGSFILE") ## ----intersfile, echo=FALSE, results="asis"----------------------------------- intersfile <- system.file("extdata", "contactCounts/Dixon_hESC_HindIII_hg18_w40000_chr1.gz", package = "FitHiC") data <- read.table(gzfile(intersfile), header=FALSE, col.names=c("Chromosome1 Name", "Mid Point 1", "Chromosome2 Name", "Mid Point 2", "Hit Count")) knitr::kable(head(data, n=6L), align = "crcrr", caption="INTERSFILE") ## ----biasfile, echo=FALSE, results="asis"------------------------------------- biasfile <- system.file("extdata", "biasPerLocus/Dixon_hESC_HindIII_hg18_w40000_chr1.gz", package = "FitHiC") data <- read.table(gzfile(biasfile), header=FALSE, col.names=c("Chromosome Name", "Mid Point", "Bias")) knitr::kable(head(data, n=6L), align = "crr", caption="BIASFILE")