Read tables of differential statistics

Usage

read_differential(
  filename,
  feature_id_column = NULL,
  pval_column = NULL,
  qval_column = NULL,
  fc_column = NULL,
  fold_change_scale = "auto",
  unlog_foldchanges = NULL
)

Arguments

filename: File name of file with table of differential statistics
feature_id_column: Column of stats file with feature identifiers
pval_column: Column of stats file with p values
qval_column: Column of stats file with adjust p values/ q values
fc_column: Column of stats with fold changes
fold_change_scale: Scale of the values in fc_column: one of "auto" (default, infer and validate from the column name and data distribution), "log2" or "linear". Whenever the resolved scale is "log2" (whether resolved automatically or declared explicitly), fc_column in the returned data frame is converted to linear scale - it will not match the raw file values. Pass "linear" for passthrough of the file's values as-is. See resolve_foldchange_scale.
unlog_foldchanges: Deprecated, use fold_change_scale instead. Reverse a log on fold changes? Set to TRUE if values are logged.

Value

output Validated selected columns of differential stats files as a data frame, with the resolved scale attached as the fold_change_scale attribute. fc_column is always on a linear scale in the returned data frame - see fold_change_scale above.

Examples

stats_file <- tempfile(fileext = ".tsv")
write.table(
  data.frame(
    gene_id = paste0("gene", 1:5),
    pvalue = c(0.001, 0.2, 0.03, 0.5, 0.008),
    padj = c(0.01, 0.4, 0.1, 0.7, 0.04),
    log2FoldChange = c(2.5, -0.1, 1.2, 0.3, -3.1)
  ),
  stats_file, sep = "\t", row.names = FALSE, quote = FALSE
)
read_differential(stats_file,
  feature_id_column = "gene_id",
  pval_column = "pvalue",
  qval_column = "padj",
  fc_column = "log2FoldChange"
)
#>       gene_id pvalue padj log2FoldChange
#> gene1   gene1  0.001 0.01       5.656854
#> gene2   gene2  0.200 0.40      -1.071773
#> gene3   gene3  0.030 0.10       2.297397
#> gene4   gene4  0.500 0.70       1.231144
#> gene5   gene5  0.008 0.04      -8.574188