Compile contrast stats for inclusion in shinyngs

Compile contrast stats for inclusion in shinyngs

Usage

compile_contrast_data(
  differential_stats_files,
  feature_id_column = NULL,
  pval_column = NULL,
  qval_column = NULL,
  fc_column = NULL,
  fold_change_scale = "auto",
  unlog_foldchanges = NULL
)

Arguments

differential_stats_files

Tabular files with differential stats

feature_id_column

Feature identifier column in stats files

pval_column

P value column in stats files

qval_column

Q value column in stats files

fc_column

Fold change column in stats files

fold_change_scale

Scale of the values in fc_column: one of "auto" (default), "log2" or "linear". Resolved once across the fold changes combined from all differential_stats_files, rather than per-file, so contrasts from the same experiment are treated consistently. Whenever the resolved scale is "log2", the fold_changes element of the returned list is converted to linear scale - it will not match the raw file values. Pass "linear" for passthrough of the files' values as-is. See resolve_foldchange_scale.

unlog_foldchanges

Deprecated, use fold_change_scale instead. Should fold change values be unlogged?

Value

output A named list of data frames by statistic (fold_changes is always on a linear scale, see fold_change_scale above; also pvals, qvals), number of columns equal to input file number