loopApaWtHic: Aggregate peak analysis of differential loop results from WT...
In EricSDavis/hictoolsr: An R Package for Hi-C Data Analysis
loopApaWtHic R Documentation
Aggregate peak analysis of differential loop results from WT Hi-C
Description
Differential loops between WT and FS conditions were called using data from
"Phase separation drives aberrant chromatin looping and cancer development"
by Ahn et al. 2021 (GEO links GSE143465 and GSE143465). Short interactions
were filtered out from all loops, WT-specific loops and FS-specific loops
and a 21x21 matrix of KR-normalized pixels at 10-kb resolution were
aggregated for each loop group from the replicate-merged Hi-C map of the
WT condition. Data is stored in "data/loopApaWtHic.rda".
Usage
data("loopApaWtHic")
Format
The data object contains a list of 3 APA matrices extracted from
a replicate-merged Hi-C map of the WT condition corresponding to all loops,
WT-specific loops, and FS-specific loops.
References
Ahn, Jeong Hyun, Eric S. Davis, Timothy A. Daugird,
Shuai Zhao, Ivana Yoseli Quiroga, Hidetaka Uryu, Jie Li,
et al. 2021. “Phase Separation Drives Aberrant Chromatin
Looping and Cancer Development.” Nature 595 (7868): 591–95.
EricSDavis/hictoolsr documentation built on Sept. 4, 2022, 12:36 a.m.
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| loopApaWtHic | R Documentation |
Aggregate peak analysis of differential loop results from WT Hi-C
Description
Differential loops between WT and FS conditions were called using data from "Phase separation drives aberrant chromatin looping and cancer development" by Ahn et al. 2021 (GEO links GSE143465 and GSE143465). Short interactions were filtered out from all loops, WT-specific loops and FS-specific loops and a 21x21 matrix of KR-normalized pixels at 10-kb resolution were aggregated for each loop group from the replicate-merged Hi-C map of the WT condition. Data is stored in "data/loopApaWtHic.rda".
Usage
data("loopApaWtHic")
Format
The data object contains a list of 3 APA matrices extracted from a replicate-merged Hi-C map of the WT condition corresponding to all loops, WT-specific loops, and FS-specific loops.
References
Ahn, Jeong Hyun, Eric S. Davis, Timothy A. Daugird, Shuai Zhao, Ivana Yoseli Quiroga, Hidetaka Uryu, Jie Li, et al. 2021. “Phase Separation Drives Aberrant Chromatin Looping and Cancer Development.” Nature 595 (7868): 591–95.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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