Basically a wrapper around readr::read_delim() but performs some initial tidying operations such as gather() rearranging columns. The label_col will be renamed to Feature.
Arguments
- file
A path to a file but can also be a connection or literal data.
- delim
The field separator or delimiter. For example "," in csv files.
- label_col
The index or name of the column that will be used to label Features. For example an identifier (e.g., KEGG, CAS, HMDB) or a m/z-RT pair.
- metadata_cols
The index/indices or name(s) of column(s) that hold additional feature metadata (e.g., retention times, additional identifiers or m/z values).
- ...
Additional arguments passed on to
readr::read_delim()
References
H. Wickham, J. Stat. Soft. 2014, 59, DOI 10.18637/jss.v059.i10.
H. Wickham, M. Averick, J. Bryan, W. Chang, L. McGowan, R. François, G. Grolemund, A. Hayes, L. Henry, J. Hester, M. Kuhn, T. Pedersen, E. Miller, S. Bache, K. Müller, J. Ooms, D. Robinson, D. Seidel, V. Spinu, K. Takahashi, D. Vaughan, C. Wilke, K. Woo, H. Yutani, JOSS 2019, 4, 1686, DOI 10.21105/joss.01686.
“12 Tidy data | R for Data Science,” can be found under https://r4ds.had.co.nz/tidy-data.html, 2023.
Examples
# Read a toy dataset in the format produced with Bruker MetaboScape (Version 2021).
featuretable_path <- system.file("extdata", "toy_metaboscape.csv", package = "metamorphr")
# Example 1: Provide indices for metadata_cols
featuretable <- read_featuretable(featuretable_path, metadata_cols = 2:5)
featuretable
#> # A tibble: 110 × 8
#> UID Feature Sample Intensity RT `m/z` Name Formula
#> <int> <chr> <chr> <dbl> <dbl> <dbl> <chr> <chr>
#> 1 1 161.10519 Da 26.98 s Sample1 4 0.45 162. NA C7H15N…
#> 2 2 276.13647 Da 27.28 s Sample1 3 0.45 277. Octyl hyd… C16H22…
#> 3 3 304.24023 Da 32.86 s Sample1 NA 0.55 305. Arachidon… C20H32…
#> 4 4 417.23236 Da 60.08 s Sample1 5 1 418. NA NA
#> 5 5 104.10753 Da 170.31 s Sample1 5 2.84 105. NA C5H14NO
#> 6 6 105.04259 Da 199.80 s Sample1 5 3.33 106. NA C3H8NO3
#> 7 7 237.09204 Da 313.24 s Sample1 NA 5.22 238. Ketamine C13H16…
#> 8 8 745.09111 Da 382.23 s Sample1 3 6.37 746. NADPH C21H30…
#> 9 9 427.02942 Da 424.84 s Sample1 4 7.08 428. ADP C10H15…
#> 10 10 1284.34904 Da 498.94 s Sample1 NA 8.32 1285. NA NA
#> # ℹ 100 more rows
# Example 2: Provide a name for label_col and indices for metadata_cols
featuretable <- read_featuretable(
featuretable_path,
label_col = "m/z",
metadata_cols = c(1, 2, 4, 5)
)
featuretable
#> # A tibble: 110 × 8
#> UID Feature Sample Intensity `Bucket label` RT Name Formula
#> <int> <chr> <chr> <dbl> <chr> <dbl> <chr> <chr>
#> 1 1 162.11302 Sample1 4 161.10519 Da 26.98 s 0.45 NA C7H15N…
#> 2 2 277.1443 Sample1 3 276.13647 Da 27.28 s 0.45 Octy… C16H22…
#> 3 3 305.24806 Sample1 NA 304.24023 Da 32.86 s 0.55 Arac… C20H32…
#> 4 4 418.24019 Sample1 5 417.23236 Da 60.08 s 1 NA NA
#> 5 5 105.11536 Sample1 5 104.10753 Da 170.31 s 2.84 NA C5H14NO
#> 6 6 106.05042 Sample1 5 105.04259 Da 199.80 s 3.33 NA C3H8NO3
#> 7 7 238.09987 Sample1 NA 237.09204 Da 313.24 s 5.22 Keta… C13H16…
#> 8 8 746.09894 Sample1 3 745.09111 Da 382.23 s 6.37 NADPH C21H30…
#> 9 9 428.03725 Sample1 4 427.02942 Da 424.84 s 7.08 ADP C10H15…
#> 10 10 1285.35687 Sample1 NA 1284.34904 Da 498.94 s 8.32 NA NA
#> # ℹ 100 more rows
# Example 3: Provide names for both, label_col and metadata_cols
featuretable <- read_featuretable(
featuretable_path,
label_col = "m/z",
metadata_cols = c("Bucket label", "RT", "Name", "Formula")
)
featuretable
#> # A tibble: 110 × 8
#> UID Feature Sample Intensity `Bucket label` RT Name Formula
#> <int> <chr> <chr> <dbl> <chr> <dbl> <chr> <chr>
#> 1 1 162.11302 Sample1 4 161.10519 Da 26.98 s 0.45 NA C7H15N…
#> 2 2 277.1443 Sample1 3 276.13647 Da 27.28 s 0.45 Octy… C16H22…
#> 3 3 305.24806 Sample1 NA 304.24023 Da 32.86 s 0.55 Arac… C20H32…
#> 4 4 418.24019 Sample1 5 417.23236 Da 60.08 s 1 NA NA
#> 5 5 105.11536 Sample1 5 104.10753 Da 170.31 s 2.84 NA C5H14NO
#> 6 6 106.05042 Sample1 5 105.04259 Da 199.80 s 3.33 NA C3H8NO3
#> 7 7 238.09987 Sample1 NA 237.09204 Da 313.24 s 5.22 Keta… C13H16…
#> 8 8 746.09894 Sample1 3 745.09111 Da 382.23 s 6.37 NADPH C21H30…
#> 9 9 428.03725 Sample1 4 427.02942 Da 424.84 s 7.08 ADP C10H15…
#> 10 10 1285.35687 Sample1 NA 1284.34904 Da 498.94 s 8.32 NA NA
#> # ℹ 100 more rows