estimate_idr2d_hic {idr2d} | R Documentation

## Estimates IDR for Genomic Interactions measured by Hi-C experiments

### Description

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.

### Usage

    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
    )

### Arguments

`rep1_df` | data frame of either parsed .hic file from Juicer (output of `parse_juicer_matrix`) or parsed .matrix and .bed files from HiC-Pro (output of `parse_hic_pro_matrix`) for replicate 1
`rep2_df` | data frame of either parsed .hic file from Juicer (output of `parse_juicer_matrix`) or parsed .matrix and .bed files from HiC-Pro (output of `parse_hic_pro_matrix`) for replicate 2
`combined_min_value` | exclude blocks with a combined (replicate 1 + replicate 2) read count or normalized read count of less than `combined_min_value` (default is 20 reads, set `combined_min_value = -Inf` to disable)
`combined_max_value` | exclude blocks with a combined (replicate 1 + replicate 2) read count or normalized read count of more than `combined_max_value` (disabled by default, set `combined_max_value = Inf` to disable)
`min_value` | exclude blocks with a read count or normalized read count of less than `min_value` in one replicate (disabled by default, set `min_value = -Inf` to disable)
`max_value` | exclude blocks with a read count or normalized read count of more than `max_value` in one replicate (disabled by default, set `max_value = Inf` to disable)
`max_factor` | numeric; controls the replacement values for `Inf` and `-Inf`. `Inf` are replaced by `max(x) * max_factor` and `-Inf` are replaced by `min(x) / max_factor`.
`jitter_factor` | numeric; controls the magnitude of the noise that is added to `x`. This is done to break ties in `x`. Set `jitter_factor = NULL` for no jitter.
`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 `est.IDR`

### Value

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

### References

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.

### Examples

    idr_results_df <- estimate_idr2d_hic(idr2d:::hic$rep1_df,
                                         idr2d:::hic$rep2_df)
    summary(idr_results_df)

[Package idr2d version 1.2.2 Index]