scan_spike_counts {spiky} | R Documentation

## run spike_counts on BAM/CRAM files and shape the results for model_glm_pmol

### Description

Typically one will want to fit a correction model to multiple samples. This function eases this task by merging the output of spike_counts into a data.frame that model_glm_pmol can directly fit.

### Usage

    scan_spike_counts(files, spike, methylated = 1, sep = "_")

### Arguments

`files` | a vector of BAM/CRAM file names
`spike` | a spike-in database
`methylated` | a logical (0/1) to include only methylated fragments
`sep` | the separator for spike-in contig names ("_")

### Value

       a data.frame with columns "frag_grp", "id", and "read_count"

### Examples

    data(spike)
    library(GenomicRanges)
    sb <- system.file("extdata", "example.spike.bam", package="spiky",
                      mustWork=TRUE)
    scan_spike_counts(sb, spike=spike)
    fit <- model_glm_pmol(scan_spike_counts(sb, spike=spike),spike=spike)

[Package spiky version 1.0.0 Index]