Description Usage Arguments Value Author(s) Examples
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.
1 2 3 4 |
fragsfile |
The path specifies where FRAGSFILE is located in the file system. FRAGSFILE 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. |
intersfile |
The path specifies where INTERSFILE is located in the file sytem. INTERSFILE 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 midPoints of the fragment pair; fifth column stands for hitCount. |
outdir |
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. |
biasfile |
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. |
noOfPasses |
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. DEFAULT is 1. |
libname |
Name of the library that is analyzed to be used for plots. DEFAULT is empty. |
distUpThres |
Upper bound on the intra-chromosomal distance range (unit: base pairs). DEFAULT is no limit. |
distLowThres |
Lower bound on the intra-chromosomal distance range (unit: base pairs). DEFAULT is no limit. |
visual |
Use this flag for generating plots. DEFAULT is False. |
useHiCPro |
Whether to use HiC-Pro preprocessed data. DEFAULT is False. |
None
Ruyu Tan, rut003@ucsd.edu
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 | 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)
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)
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)
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)
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)
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)
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, useHiCPro=TRUE)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.