Description Details Objects from the Class Slots Methods Author(s) See Also Examples

A class for representing high throughput Chromosome Conformation Capture data from next-generation sequencing experiments.

The `normPerExpected`

method estimates the expected interactions based on a the dependency on the genomic
proximity between two loci. See `getExpectedCounts`

function for details.

The `normPerTrans`

method is based on the assumption that all trans contacts should be the same. Thus, the cis contacts can be normalized by the interaction level of trans data.
The `xtrans`

trans map has to share its 'xgi' ranges with the
cis map, and the `ytrans`

has to share its 'ygi' ranges with
the cismap.
The `method`

is used to combine the normalization factor from x
and y ranges. Must be ‘sum’, ‘mult’ or ‘mean’.

Objects can be created either by:

calls of the form

`new("HTCexp", intdata, GRanges, GRanges)`

.using the auxiliary function

`HTCexp`

and supplying contact Matrix with x and y intervals definition. The forceSymmetric option can used to force intra-chromosomal contact maps to be stored as symmetrical matrix.

`intdata`

:Dense or Sparse Matrix, holding the interaction level between each pairs of 'x-y' intervals. The 'y' intervals must be in rows, and the 'x' in columns.

`ygi`

:Genomic ranges of y intervals; see class

`granges`

for details`xgi`

:Genomic ranges of x intervals; see class

`granges`

for details

- c(x, ...)
Combines 'x' and the

`signature("HTCexp")`

objects in '...' together. The results is an object of class`signature("HTCList")`

- detail(x)
`signature("HTCexp")`

: a more detailed output of the experiment than provided by`show`

.- divide(x)
comparison of two

`signature("HTCexp")`

objects. Perform the division of the two contact matrices on the common 'x' and 'y' intervals. The operation is done only on the common intervals of both objects. If one of the two objects has a count to zero, the divided value will be NA- intdata(x)
return the

`intdata`

Matrix counts. Note that triangular matrices are always returned as symmetric matrices.- export(x)
Defunct. See exportC method

- isBinned
return TRUE if the data are binned. The method tests if the 'x' and 'y' genome intervals are the same, if 90% of the bins have the same size and if the full genomic range is covered

- forceSymmetric(x)
force the interaction data to 'symmetricMatrix'

- forceTriangular(x)
force the interaction data to triangular, ie. symmetric. Lower triangle of the matrix is set to zero, therefore reducing the size of the data in memory

- isIntraChrom(x)
return TRUE if the current

`signature("HTCexp")`

object contains intrachromosomal contact data- isSymmetric(x)
return TRUE if the contact map is symmetrical, i.e inherits the

`symmetricMatrix`

class- normPerReads(x)
normalize the contact matrix by the total number of reads of the matrix.

- normPerExpected(x, ...)
normalize the contact matrix by the expected number of reads based on the distance between two loci. See details.

- normPerZscore(x)
Defunct. See normPerExpected method

- normPerTrans(x, xtrans, ytrans, method="sum")
Normalize cis contact map based on the trans interactions. See details

- plot(x)
visualization method; Display an heatmap of the contact data. Refer to the documentation of

`mapC`

for more details of the plotting function- range(x)
return the genomic range of the

`signature("HTCexp")`

object- seq_name(x)
Defunct. See seqlevels method

- seqlevels(x)
return the sequence levels of the

`signature("HTCexp")`

object- show(x)
summarized output of the experiment, with informations about the data dimension and the genomic region studied

- substract(x)
comparison of two

`signature("HTCexp")`

objects. Perform the substraction of the two contact matrices on the common 'x' and 'y' intervals. The operation is done only on the common intervals of both objects. If one of the two objects has a count to zero, the divided value will be NA- summary(x)
return descriptive summary statistics about the contact map

- x_intervals(x)
return the

`xgi`

GRanges object defining the x intervals- y_intervals(x)
return the

`ygi`

GRanges object defining the y intervals- xy_intervals(x)
return both

`xgi`

and`ygi`

objects as a`GRangesList`

object

Nicolas Servant

`GRanges-class`

,`GRangesList-class`

,`Matrix-class`

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 | ```
data(Nora_5C)
## HTCexp descriptio
show(E14)
detail(E14)
## Is binned data ?
isBinned(E14$chrXchrX)
## Is a inter or intrachromsomal experiment ?
isIntraChrom(E14$chrXchrX)
## Bin the data
E14.bin <- binningC(E14$chrXchrX, binsize=100000, step=3)
## Divide by expected interaction counts
E14norm<-normPerExpected(E14.bin)
## Operation on HTCexp object
E14_d_MEF<-divide(normPerReads(E14$chrXchrX), normPerReads(MEF$chrXchrX))
E14_s_MEF<-substract(normPerReads(E14$chrXchrX), normPerReads(MEF$chrXchrX))
## Overlap with genomic annotation
require(rtracklayer)
gene <- import(file.path(system.file("extdata", package="HiTC"),"refseq_mm9_chrX_98831149_103425150.bed"), format="bed")
plot(E14$chrXchrX, tracks=list(RefSeqGene=gene))
## Not run:
## normPerTrans data normalization applied on \href{http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeUmassDekker5C}{ENCODE data}.
ENCODE=import.my5C("./ENM-GM12878-R1.matrix")
## Look at raw contact map
mapC(ENCODE$chr7chr7)
## look at normalize by trans contact map
mapC(normPerTrans(ENCODE$chr7chr7, xtrans=ENCODE$chr7chr5, ytrans=ENCODE$chr5chr7))
## End(Not run)
## Not run:
## Export
exportC(E14$chrXchrX, con="E14.csv")
## End(Not run)
``` |

bioinfo-pf-curie/HiTC documentation built on May 17, 2019, 6:39 p.m.

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