Import genome coverage matrix files

Import genome coverage matrix files

coverage_matrix2nmat(
  x = NULL,
  filename = NULL,
  signal_name = NULL,
  target_name = "target",
  background = 0,
  smooth = FALSE,
  target_is_single_point = FALSE,
  signal_is_categorical = FALSE,
  mat_grep = "[-0-9]+:[-0-9]+",
  upstream_grep = "^[-]",
  downstream_grep = "^[^-]",
  target_grep = "^0$",
  verbose = FALSE,
  ...
)

Arguments

x

data.frame or compatible object containing genome coverage data, or a character file path. When x is not supplied, filename is used to import data. When x is a filename, it is used to populate filename, then data is imported into x.

filename

character path to a genome coverage file. When x is supplied, this argument is ignored. When filename is used, only the first file is imported.

signal_name

The name of signal regions. It is only used for printing the object. When signal_name is NULL, the signal_name is derived from names(filename) if available, then basename(filename), or "signal" then only x is supplied.

target_name

The name of the target names. It is only used for printing the object.

background

numeric value containing the background value in the matrix.

smooth

logical whether to apply smoothing on rows.

target_is_single_point, signal_is_categorical

logical indicating whether the target region is a single point, and whether signal matrix is categorical, respectively.

mat_grep

character regular expression pattern used to identify colnames which contain coverage data. The default pattern expects the format "-200:-100".

upstream_grep

character regular expression pattern used to identify upstream colnames from values that match mat_grep. The default assumes any region beginning "-" is negative and upstream the central target region.

downstream_grep

character regular expression pattern used to identify upstream colnames from values that match mat_grep. The default assumes all colnames which are not upstream are therefore downstream.

target_grep

character regular expression pattern used to identify a colname referring to the target, which by default can only be "0". Otherwise, no target region is defined.

verbose

logical indicating whether to print verbose output.

...

additional arguments are ignored.

Value

normalizedMatrix numeric matrix, where additiona metadata is stored in the object attributes. See EnrichedHeatmap::as.normalizedMatrix() for more details about the metadata. The rownames are defined by the first colname which does not match mat_grep, which by default is "Gene ID", otherwise rownames are NULL.

Details

This function imports genome coverage data matrix and returns an object of class normalizedMatrix compatible for use by the package "EnrichedHeatmap".

There is a conversion function EnrichedHeatmap::as.normalizedMatrix(), however this function does not call that function, in favor of defining the attributes directly. In future, this function may change to call that function.

See also

Other jam coverage heatmap functions: get_nmat_ceiling(), nmathm_row_order(), nmatlist2heatmaps(), validate_heatmap_params(), zoom_nmatlist(), zoom_nmat()

Other jam import functions: deepTools_matrix2nmat(), frequency_matrix2nmat(), import_lipotype_csv(), import_metabolomics_niehs(), import_nanostring_csv(), import_nanostring_rcc(), import_nanostring_rlf(), import_proteomics_PD(), import_proteomics_mascot(), import_salmon_quant(), process_metab_compounds_file()

Examples

## There is a small example file to use for testing
cov_file <- system.file("data", "tss_coverage.matrix", package="platjam");
cov_file <- system.file("data", "h3k4me1_coverage.matrix", package="platjam");
if (length(cov_file) > 0) {
   nmat <- coverage_matrix2nmat(cov_file);
   jamba::printDebug("signal_name: ",
      attr(nmat, "signal_name"));

if (suppressPackageStartupMessages(require(EnrichedHeatmap))) {
   color <- "red3";
   signal_name <- attr(nmat, "signal_name");
   k <- 6;
   set.seed(123);
   partition <- kmeans(log10(1+nmat), centers=k)$cluster;
   EH <- EnrichedHeatmap(log10(1+nmat),
      split=partition,
      pos_line=FALSE,
      use_raster=TRUE,
      col=jamba::getColorRamp(color, n=10),
      top_annotation=HeatmapAnnotation(
         lines=anno_enriched(gp=grid::gpar(col=colorjam::rainbowJam(k)))
      ),
      axis_name_gp=grid::gpar(fontsize=8),
      name=signal_name,
      column_title=signal_name
   );
   PHM <- Heatmap(partition,
      use_raster=TRUE,
      col=structure(colorjam::rainbowJam(k),
         names=as.character(seq_len(k))),
      name="partition",
      show_row_names=FALSE,
      width=grid::unit(3, "mm"));
   draw(PHM + EH, main_heatmap=2);
}
}
#> ##  (12:31:34) 21Sep2023:   signal_name: h3k4me1_coverage.matrix