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Basic methods for a nacho object

Source: R/methods.R
nacho-methods.Rd

Basic methods for a nacho object

Usage

print(x)
format(x)
summary(object)
dim(x)
as.data.frame(x, long = FALSE)
x[i, j]

Arguments

  • x, object: A nacho object.

  • long: If TRUE, as.data.frame() returns one row per probe and sample (the NACHO 2 $nacho layout) instead of one row per sample.

  • i: Probes to keep.

  • j: Samples to keep.

Examples

data(GSE74821)
print(GSE74821)
#> <nacho> 48 samples, 72 probes, from single-sample RCC files
#> Normalisation: GLM, with 8 housekeeping genes
#> Flagged samples: 0 of 48
#> Created with NACHO 2.0.7.9000
summary(GSE74821)
#>                  metric lower upper n_fail n_missing
#> 1                    BD  0.05  2.25      0         0
#> 2                   FoV 75.00    NA      0         0
#> 3                   PCL  0.95    NA      0         0
#> 4                   LoD  2.00    NA      0         0
#> 5       Positive_factor  0.30  3.00      0         0
#> 6          House_factor  0.10 10.00      0         0
#> 7 Housekeeping_detected  3.00    NA      0         0
dim(GSE74821)
#> [1] 72 48
head(as.data.frame(GSE74821, long = TRUE)[, 1:5])
#>                                                               IDFILE
#> 1 GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 2 GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 3 GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 4 GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 5 GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#> 6 GSM1934697_20111102_20111102-9741-1_LGWU101986-1036378WU_02.RCC.gz
#>                  title geo_accession                status submission_date
#> 1 LGWU101986-1036378WU    GSM1934697 Public on Nov 10 2015     Nov 09 2015
#> 2 LGWU101986-1036378WU    GSM1934697 Public on Nov 10 2015     Nov 09 2015
#> 3 LGWU101986-1036378WU    GSM1934697 Public on Nov 10 2015     Nov 09 2015
#> 4 LGWU101986-1036378WU    GSM1934697 Public on Nov 10 2015     Nov 09 2015
#> 5 LGWU101986-1036378WU    GSM1934697 Public on Nov 10 2015     Nov 09 2015
#> 6 LGWU101986-1036378WU    GSM1934697 Public on Nov 10 2015     Nov 09 2015
GSE74821[, 1:12]
#> <nacho> 12 samples, 72 probes, from single-sample RCC files
#> Normalisation: GLM, with 8 housekeeping genes
#> Flagged samples: 0 of 12
#> Created with NACHO 2.0.7.9000