Package FitHiC. October 16, 2018
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1 Type Package Package FitHiC October 16, 2018 Title Confidence estimation for intra-chromosomal contact maps Version Date Description Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C. License GPL (>= 2) biocviews DNA3DStructure, Software Imports data.table, fdrtool, grdevices, graphics, Rcpp, stats, utils LinkingTo Rcpp RoxygenNote Suggests knitr, rmarkdown VignetteBuilder knitr git_url git_branch RELEASE_3_7 git_last_commit 4777b02 git_last_commit_date Date/Publication Author Ferhat Ay [aut] (Python original, Timothy L. Bailey [aut], William S. Noble [aut], Ruyu Tan [aut, cre, trl] (R port) Maintainer Ruyu Tan <rut003@ucsd.edu> R topics documented: FitHiC Index 5 1
2 2 FitHiC FitHiC Fit-Hi-C Description Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C. Usage biasfile = "none", noofpasses = 1, noofbins = 100, mappabilitythreshold = 1, libname = "", distupthres = -1, distlowthres = -1, visual = FALSE, usehicpro = FALSE) Arguments fragsfile intersfile outdir biasfile noofpasses The path specifies where FRAGSFILE is located in the file system. FRAGS- FILE stores the information about midpoints (or start indices) of the fragments. It should consist of 5 columns: first column stands for chromosome name; third column stands for the midpoint; fourth column stands for the hitcount; second column and fifth column can be arbitrary. The path specifies where INTERSFILE is located in the file sytem. INTERS- FILE stores the information about interactions between fragment pairs. It should consist of 5 columns: first column and third column stand for the chromosome names of the fragment pair; second column and fourth column stand for mid- Points of the fragment pair; fifth column stands for hitcount. The path specifies where the output files will be stored in the file system. If the path does not exist, it will be automatically created. The path specifies where BIASFILE is located in the file system. BIASFILE stores the information about biases calculated by ICE for each locus. It should consist of 3 columns: first column stands for chromosome name; second column stands for the midpoint; third column stands for the bias. This argument is OPTIONAL. Number of passes after the initial (before) fit. DEFAULT is 1 (after). noofbins Number of equal-occupancy (count) bins. Default is 100. mappabilitythreshold Minimum number of hits per locus that has to exist to call it mappable. DE- FAULT is 1. libname distupthres distlowthres visual usehicpro Name of the library that is analyzed to be used for plots. DEFAULT is empty. Upper bound on the intra-chromosomal distance range (unit: base pairs). DE- FAULT is no limit. Lower bound on the intra-chromosomal distance range (unit: base pairs). DE- FAULT is no limit. Use this flag for generating plots. DEFAULT is False. Whether to use HiC-Pro preprocessed data. DEFAULT is False.
3 FitHiC 3 Value None Author(s) Ruyu Tan, <rut003@ucsd.edu> Examples "fragmentlists/duan_yeast_ecori.gz", "contactcounts/duan_yeast_ecori.gz", outdir <- file.path(getwd(), "Duan_yeast_EcoRI") libname="duan_yeast_ecori", distupthres=250000, distlowthres=10000) "fragmentlists/duan_yeast_hindiii.gz", "contactcounts/duan_yeast_hindiii.gz", outdir <- file.path(getwd(), "Duan_yeast_HindIII") libname="duan_yeast_hindiii", distupthres=250000, distlowthres=10000) "fragmentlists/dixon_hesc_hindiii_hg18_combinefrags10_chr1.gz", "contactcounts/dixon_hesc_hindiii_hg18_combinefrags10_chr1.gz", outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_combineFrags10_chr1") libname="dixon_hesc_hindiii_hg18_combinefrags10_chr1", noofbins=200, "fragmentlists/dixon_mesc_hindiii_mm9_combinefrags10_chr1.gz", "contactcounts/dixon_mesc_hindiii_mm9_combinefrags10_chr1.gz", outdir <- file.path(getwd(), "Dixon_mESC_HindIII_mm9_combineFrags10_chr1") libname="dixon_mesc_hindiii_mm9_combinefrags10_chr1", noofbins=200, "fragmentlists/dixon_hesc_hindiii_hg18_w40000_chr1.gz", "contactcounts/dixon_hesc_hindiii_hg18_w40000_chr1.gz", outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_w40000_chr1") libname="dixon_hesc_hindiii_hg18_w40000_chr1", noofbins=50,
4 4 FitHiC "fragmentlists/dixon_hesc_hindiii_hg18_w40000_chr1.gz", "contactcounts/dixon_hesc_hindiii_hg18_w40000_chr1.gz", outdir <- file.path(getwd(), "Dixon_hESC_HindIII_hg18_w40000_chr1.afterICE") biasfile <- system.file("extdata", "biasperlocus/dixon_hesc_hindiii_hg18_w40000_chr1.gz", biasfile, libname="dixon_hesc_hindiii_hg18_w40000_chr1", noofbins=50, "fragmentlists/data_ _abs.bed.gz", "contactcounts/data_ matrix.gz", biasfile <- system.file("extdata", "biasperlocus/data_ _iced.matrix.biases.gz", outdir <- file.path(getwd(), "data_ ") biasfile, libname="data_ ", distupthres= , distlowthres= , usehicpro=true)
5 Index FitHiC, 2 5
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