estimate_idr2d_hic {idr2d} | R Documentation |
This method estimates Irreproducible Discovery Rates (IDR) of genomic interactions between two replicates of Hi-C experiments.
Before calling this method, call Juicer .hic contact matrix c
The contact matrix is subdivided into blocks, where the block size is
determined by resolution
. The reads per block are used to rank blocks
and replicate blocks are easily matched by genomic location.
estimate_idr2d_hic( rep1_df, rep2_df, combined_min_value = 30, combined_max_value = Inf, min_value = -Inf, max_value = Inf, max_factor = 1.5, jitter_factor = 1e-04, mu = 0.1, sigma = 1, rho = 0.2, p = 0.5, eps = 0.001, max_iteration = 30, local_idr = TRUE )
rep1_df |
data frame of either parsed .hic file from Juicer (output of
|
rep2_df |
data frame of either parsed .hic file from Juicer (output of
|
combined_min_value |
exclude blocks with a combined (replicate 1 +
replicate 2) read count or normalized read count of less than
|
combined_max_value |
exclude blocks with a combined (replicate 1 +
replicate 2) read count or normalized read count of more than
|
min_value |
exclude blocks with a read count or normalized read count
of less than |
max_value |
exclude blocks with a read count or normalized read count
of more than |
max_factor |
numeric; controls the replacement values for |
jitter_factor |
numeric; controls the magnitude of the noise that
is added to |
mu |
a starting value for the mean of the reproducible component. |
sigma |
a starting value for the standard deviation of the reproducible component. |
rho |
a starting value for the correlation coefficient of the reproducible component. |
p |
a starting value for the proportion of reproducible component. |
eps |
Stopping criterion. Iterations stop when the increment of log-likelihood is < eps*log-likelihood, Default=0.001. |
max_iteration |
integer; maximum number of iterations for IDR estimation (defaults to 30) |
local_idr |
see |
Data frame with the following columns:
column 1: | interaction | character; genomic location of
interaction block (e.g., "chr1:204940000-204940000" ) |
column 2: | value | numeric; p-value, FDR, or heuristic used to rank the interactions |
column 3: | "rep_value" | numeric; value of corresponding replicate interaction |
column 4: | "rank" | integer; rank of the interaction, established by value column, ascending order |
column 5: | "rep_rank" | integer; rank of corresponding replicate interaction |
column 6: | "idr" | integer; IDR of the block and the corresponding block in the other replicate |
Q. Li, J. B. Brown, H. Huang and P. J. Bickel. (2011) Measuring reproducibility of high-throughput experiments. Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779.
idr_results_df <- estimate_idr2d_hic(idr2d:::hic$rep1_df, idr2d:::hic$rep2_df) summary(idr_results_df)