Question: Contact Maps Of Hi-C
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gravatar for cheater149
7.8 years ago by
cheater14960
cheater14960 wrote:
Total possible interactions =chr length-genomic distance.
Genome wide average(gwa)= total interactions for all chromosomes at distance(s)/(L1-s + L2 -s ....+Ln -s).
Intrachromosomal expected = gwa(s( distance between mid points of loci)).
Intrachromosomal M*(normalised)=observed inetractions /intra expected.
Intrachromosomal correlation matrix =pearson correlation(intrachr (obs/exp) locus ,interchrom locus).
Interchromosomal matrix (23X23)expected=(i chr interaction/total i interactions)*(j chr interaction/total j interactions)* total interchromosomal inetractions.
Interchromosomal matrix(23X23)=observed i,j interactions /expected..
interchromosomal M* = expected=(i loci interaction/total i interactions)*(j loci interaction/total j interactions)* total interchromosomal inetractions.
Interchromosomal matrix=observed i,j interactions /expected..
Interchromosomal correlation matrix =pearson correlation(interchromosomal i,j values)without intra chromosomal values..
Interchromosomal averages=observed interactions b/w loci on chr pair/possible interactions b/w chromosomes (product of loci on each chr)

for multiple pairings numerator and denominatr summed.

sir these are the mathematical calculations i made for Hi-C contact map study.are these correct and please can any one enlighten me on inter chromosomal averages.Im putting it in order to verify whether the calculations are correct with respect to Lieberman data.

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ADD COMMENTlink modified 7.8 years ago by Istvan Albert ♦♦ 85k • written 7.8 years ago by cheater14960

Total possible interactions =chr length-genomic distance .... i don`t understand this at all ... that should be all the possible restriction fragments ^ 2

ADD REPLYlink written 7.8 years ago by Gjain5.5k

sir ,but when we consider as a genomic distance based interactions then i think it would be so...which im thinking from the supplementary statement.(The possible number of pairs of genomic positions separated by d on a given chromosome is Lc-d, where Lc is the length of the chromosome.)

ADD REPLYlink written 7.8 years ago by cheater14960

what is your experiment ... do you have any HiC dataset ... how did you get that data?

ADD REPLYlink written 7.8 years ago by Gjain5.5k

sir ..im working on GSE18199 and GSE35156 SRA data sets. i want to understand the process exactly...

ADD REPLYlink written 7.8 years ago by cheater14960

Please read the paper and supplementary text again and try to understand how the data is generated. Before defining mathematically you need to understand theoretically what is an interaction when you are talking about HiC.

ADD REPLYlink written 7.8 years ago by Gjain5.5k

I am changing the type to question since it seems that a lot of discussions is taking place that are only visible to moderators

ADD REPLYlink modified 7.8 years ago • written 7.8 years ago by Istvan Albert ♦♦ 85k
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