.read_rectangles {autonomics}R Documentation

Read omics data from rectangular file

Description

Read omics data from rectangular file

Usage

.read_rectangles(
  file,
  sheet = 1,
  fid_rows,
  fid_cols,
  sid_rows,
  sid_cols,
  expr_rows,
  expr_cols,
  fvar_rows = NULL,
  fvar_cols = NULL,
  svar_rows = NULL,
  svar_cols = NULL,
  fdata_rows = NULL,
  fdata_cols = NULL,
  sdata_rows = NULL,
  sdata_cols = NULL,
  transpose = FALSE,
  verbose = TRUE
)

read_rectangles(
  file,
  sheet = 1,
  fid_rows,
  fid_cols,
  sid_rows,
  sid_cols,
  expr_rows,
  expr_cols,
  fvar_rows = NULL,
  fvar_cols = NULL,
  svar_rows = NULL,
  svar_cols = NULL,
  fdata_rows = NULL,
  fdata_cols = NULL,
  sdata_rows = NULL,
  sdata_cols = NULL,
  transpose = FALSE,
  sfile = NULL,
  sfileby = NULL,
  subgroupvar = character(0),
  verbose = TRUE
)

Arguments

file

string: name of text (txt, csv, tsv, adat) or excel (xls, xlsx) file

sheet

integer/string: only relevant for excel files

fid_rows

numeric vector: featureid rows

fid_cols

numeric vector: featureid cols

sid_rows

numeric vector: sampleid rows

sid_cols

numeric vector: sampleid cols

expr_rows

numeric vector: expr rows

expr_cols

numeric vector: expr cols

fvar_rows

numeric vector: fvar rows

fvar_cols

numeric vector: fvar cols

svar_rows

numeric vector: svar rows

svar_cols

numeric vector: svar cols

fdata_rows

numeric vector: fdata rows

fdata_cols

numeric vector: fdata cols

sdata_rows

numeric vector: sdata rows

sdata_cols

numeric vector: sdata cols

transpose

TRUE or FALSE (default)

verbose

TRUE (default) or FALSE

sfile

sample file

sfileby

sample file mergeby column

subgroupvar

subgroupvar in sfile

Value

SummarizedExperiment

Examples

# RNASEQ
   file <- download_data('billing16.rnacounts.txt')
   read_rectangles(file,fid_rows   = 2:58736,   fid_cols   = 1,
                   sid_rows   = 1,         sid_cols   = 4:14,
                   expr_rows  = 2:58736,   expr_cols  = 4:14,
                   fvar_rows  = 1,         fvar_cols  = 1:3,
                   fdata_rows = 2:58736,   fdata_cols = 1:3,
                   transpose  = FALSE)
# LCMSMS PROTEINGROUPS
   file <- download_data('billing19.proteingroups.txt')
   read_rectangles(file,fid_rows   = 2:9044,  fid_cols   = 383,
                   sid_rows   = 1,       sid_cols   = seq(124, 316, by = 6),
                   expr_rows  = 2:9044,  expr_cols  = seq(124, 316, by = 6),
                   fvar_rows  = 1,       fvar_cols  = c(2, 6, 7, 383),
                   fdata_rows = 2:9044,  fdata_cols = c(2, 6, 7, 383),
                   transpose  = FALSE)
# SOMASCAN
   file <- download_data('billing16.somascan.adat')
   read_rectangles(file,fid_rows   = 21,       fid_cols   = 19:1146,
                   sid_rows   = 30:40,    sid_cols   = 4,
                   expr_rows  = 30:40,    expr_cols  = 19:1146,
                   fvar_rows  = 21:28,    fvar_cols  = 18,
                   svar_rows  = 29,       svar_cols  = 1:17,
                   fdata_rows = 21:28,    fdata_cols = 19:1146,
                   sdata_rows = 30:40,    sdata_cols = 1:17,
                   transpose  = TRUE)
# METABOLON
   file <- download_data('halama18.metabolon.xlsx')
   read_rectangles(file, sheet = 2,
                   fid_rows   = 11:401,    fid_cols   = 5,
                   sid_rows   = 3,         sid_cols   = 15:86,
                   expr_rows  = 11:401,    expr_cols  = 15:86,
                   fvar_rows  = 10,        fvar_cols  = 1:14,
                   svar_rows  = 1:10,      svar_cols  = 14,
                   fdata_rows = 11:401,    fdata_cols = 1:14,
                   sdata_rows = 1:10,      sdata_cols = 15:86,
                   transpose  = FALSE)

[Package autonomics version 1.1.7 Index]