.read_rectangles {autonomics} | R Documentation |
Read omics data from rectangular file
.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 )
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 |
SummarizedExperiment
# 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)