Select or rename columns in a qseaSet sample table

Extends dplyr::select() to keep or rename columns in a qseaSet's sampleTable. This allows column subsetting, renaming, and use of tidyselect helpers while preserving key identifiers.

# S3 method for class 'qseaSet'
select(.data, ...)

Arguments

.data

qseaSet. A qseaSet object whose sampleTable columns will be selected or renamed.

...

Additional arguments passed to dplyr::select(), supports tidyselect helpers (e.g., dplyr::matches(), dplyr::starts_with()). Negative selection (-col) is supported, but sample_name and group cannot be removed. Default: none.

Value

A qseaSet with its sampleTable updated:

• contains only selected/renamed columns,

• always includes sample_name and group (if available).

Details

This is a wrapper around selectQset(). Essential columns sample_name and group are always preserved (and appear first if present).

See also

selectQset() for the underlying implementation, qsea::getSampleTable() to view results, mutate.qseaSet(), filter.qseaSet() for related dplyr verbs.

Examples

data(exampleTumourNormal, package = "mesa")

# Keep only specific columns (sample_name and group always preserved)
exampleTumourNormal %>%
    dplyr::select(type, tumour) %>%
    qsea::getSampleTable()
#>          sample_name    group        type tumour
#> Colon1_N    Colon1_N Colon1_N NormalColon Normal
#> Colon1_T    Colon1_T Colon1_T         CRC Tumour
#> Colon2_N    Colon2_N Colon2_N NormalColon Normal
#> Colon2_T    Colon2_T Colon2_T         CRC Tumour
#> Lung1_N      Lung1_N  Lung1_N  NormalLung Normal
#> Lung1_T      Lung1_T  Lung1_T        LUAD Tumour
#> Lung2_N      Lung2_N  Lung2_N  NormalLung Normal
#> Lung2_T      Lung2_T  Lung2_T        LUSC Tumour
#> Lung3_N      Lung3_N  Lung3_N  NormalLung Normal
#> Lung3_T      Lung3_T  Lung3_T        LUAD Tumour

# Select and rename a column
exampleTumourNormal %>%
    dplyr::select(age, tumour_new = tumour) %>%
    qsea::getSampleTable()
#>          sample_name    group age tumour_new
#> Colon1_N    Colon1_N Colon1_N  80     Normal
#> Colon1_T    Colon1_T Colon1_T  80     Tumour
#> Colon2_N    Colon2_N Colon2_N  67     Normal
#> Colon2_T    Colon2_T Colon2_T  67     Tumour
#> Lung1_N      Lung1_N  Lung1_N  64     Normal
#> Lung1_T      Lung1_T  Lung1_T  64     Tumour
#> Lung2_N      Lung2_N  Lung2_N  71     Normal
#> Lung2_T      Lung2_T  Lung2_T  71     Tumour
#> Lung3_N      Lung3_N  Lung3_N  72     Normal
#> Lung3_T      Lung3_T  Lung3_T  72     Tumour

# Use tidyselect helpers
exampleTumourNormal %>%
    dplyr::select(matches("s")) %>%
    qsea::getSampleTable()
#>          sample_name    group tissue stage
#> Colon1_N    Colon1_N Colon1_N  Colon  <NA>
#> Colon1_T    Colon1_T Colon1_T  Colon   III
#> Colon2_N    Colon2_N Colon2_N  Colon  <NA>
#> Colon2_T    Colon2_T Colon2_T  Colon    IV
#> Lung1_N      Lung1_N  Lung1_N   Lung  <NA>
#> Lung1_T      Lung1_T  Lung1_T   Lung   IIA
#> Lung2_N      Lung2_N  Lung2_N   Lung  <NA>
#> Lung2_T      Lung2_T  Lung2_T   Lung    IA
#> Lung3_N      Lung3_N  Lung3_N   Lung  <NA>
#> Lung3_T      Lung3_T  Lung3_T   Lung    IB

# Negative selection (except essential columns)
exampleTumourNormal %>%
    dplyr::select(-matches("s")) %>%
    qsea::getSampleTable()
#>          sample_name    group patient        type tumour age gender
#> Colon1_N    Colon1_N Colon1_N  Colon1 NormalColon Normal  80      F
#> Colon1_T    Colon1_T Colon1_T  Colon1         CRC Tumour  80      F
#> Colon2_N    Colon2_N Colon2_N  Colon2 NormalColon Normal  67      F
#> Colon2_T    Colon2_T Colon2_T  Colon2         CRC Tumour  67      F
#> Lung1_N      Lung1_N  Lung1_N   Lung1  NormalLung Normal  64      F
#> Lung1_T      Lung1_T  Lung1_T   Lung1        LUAD Tumour  64      F
#> Lung2_N      Lung2_N  Lung2_N   Lung2  NormalLung Normal  71      F
#> Lung2_T      Lung2_T  Lung2_T   Lung2        LUSC Tumour  71      F
#> Lung3_N      Lung3_N  Lung3_N   Lung3  NormalLung Normal  72      M
#> Lung3_T      Lung3_T  Lung3_T   Lung3        LUAD Tumour  72      M