NAME

Bio::Gonzales::SummarizedExperiment - represent experimental matrix-like data (assay) with features and sample info

SYNOPSIS

DESCRIPTION

http://bioconductor.org/packages/devel/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html

ATTRIBUTES

assay

    my $assay = $se->assay;

Return the assay of the summarized experiment.

col_data

    my $col_data = $se->col_data;
    $se->col_data(\@col_data);

row_data

row_names

col_names

row_data_names

col_data_names

meta_data

METHODS

data

    my $assay = $se->data;

A alias for assay.

add_col

add_cols

add_rows

aggregate

$se = $se->aggregate_by_idcs(\@idcs, sub { ... }, \@col_names)

The callback gets passed the grouping keys, rows and row indices. $_ is set to the group has that comes from the (internally used) $se->group function.

    sub {
      my ($key, $rows, $row_idcs) = @_;
      my $group = $_;
    }

$se = $se->aggregate_by_names(\@names, sub { ... }, \@col_names)

apply

as_hash

cbind

clone

col_apply

col_idx

col_idx_map

    my $I = $se->col_idx_map;
    my %I = $se->col_idx_map;

Returns a hash that maps the column names to their column index. col_idx_map is context sensitve and returns a hash in list context and a hash reference in scalar context.

col_idx_match

col_names_to_idcs

col_rename

dim

each

extract_col_by_idx

extract_col_by_name

group

group_by_idcs

group_by_names

has_col_data

has_col_names =head2 has_row_data =head2 has_row_names =head2 header =head2 header_idx =head2 header_idx_match =head2 inconsistencies =head2 json_spew =head2 make_consistent =head2 merge =head2 names_to_idcs =head2 ncol =head2 nrow =head2 rbind =head2 row_apply =head2 row_idx =head2 row_idx_map =head2 row_idx_match =head2 shuffle

slice_by_idcs

    $se->slice_by_idcs(\@idcs);
    $se->slice_by_idcs([0,5,13]);

Extract a column-"slice" from the summarized experiment. The indices select the columns.

slice_by_names

slurp_assay

    my $se = Bio::Gonzales::SummarizedExperiment->slurp_assay($source, \%params);
    my $se = Bio::Gonzales::SummarizedExperiment->slurp_assay("data.csv", { header => 1, sep => ';' });

Create a new summarized experiment from matrix/tabular data.

sort =head2 spew_assay =head2 subset =head2 encode_as_json =head2 transpose =head2 uniq

LIMITATIONS

NOTES

By convention,

• constructor or function arguments ending in ? are optional

• methods ending in ! will modify the object it is called on

SEE ALSO

AUTHOR

jw bargsten, <jwb at cpan dot org>

cpanm Bio::Gonzales

perl -MCPAN -e shell
install Bio::Gonzales