straw: straw
In mervesa/HiCDCPlus: Hi-C Direct Caller Plus
straw R Documentation
straw
Description
Adapted C++ implementation of Juicer's dump. Reads the .hic file, finds the
appropriate matrix and slice of data, and outputs as an R DataFrame.
Usage
straw(norm, fn, ch1, ch2, u, bs)
Arguments
norm
Normalization to apply. Must be one of NONE/VC/VC_SQRT/KR.
VC is vanilla coverage, VC_SQRT is square root of vanilla coverage,
and KR is Knight-Ruiz or Balanced normalization.
fn
path to the .hic file
ch1
first chromosome location (e.g., "1")
ch2
second chromosome location (e.g., "8")
u
BP (BasePair) or FRAG (restriction enzyme FRAGment)
bs
The bin size. By default, for BP, this is one of
<2500000, 1000000, 500000,
250000, 100000, 50000, 25000, 10000, 5000> and for FRAG this is one of
<500, 200,
100, 50, 20, 5, 2, 1>.
Details
Usage: straw <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize>
Value
Data.frame of a sparse matrix of data from hic file. x,y,counts
mervesa/HiCDCPlus documentation built on June 8, 2022, 3:43 a.m.
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| straw | R Documentation |
straw
Description
Adapted C++ implementation of Juicer's dump. Reads the .hic file, finds the appropriate matrix and slice of data, and outputs as an R DataFrame.
Usage
straw(norm, fn, ch1, ch2, u, bs)
Arguments
norm |
Normalization to apply. Must be one of NONE/VC/VC_SQRT/KR. VC is vanilla coverage, VC_SQRT is square root of vanilla coverage, and KR is Knight-Ruiz or Balanced normalization. |
fn |
path to the .hic file |
ch1 |
first chromosome location (e.g., "1") |
ch2 |
second chromosome location (e.g., "8") |
u |
BP (BasePair) or FRAG (restriction enzyme FRAGment) |
bs |
The bin size. By default, for BP, this is one of <2500000, 1000000, 500000, 250000, 100000, 50000, 25000, 10000, 5000> and for FRAG this is one of <500, 200, 100, 50, 20, 5, 2, 1>. |
Details
Usage: straw <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize>
Value
Data.frame of a sparse matrix of data from hic file. x,y,counts
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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