hd_filter_by_sex() filters the data and metadata by the metadata Sex variable and a specified value.
It can be used in cases of sex specific diseases before running differential expression or classification analysis.
Arguments
- dat
An HDAnalyzeR object or a dataset in wide format and sample ID as its first column.
- metadata
A dataset containing the metadata information with the sample ID as the first column. If a HDAnalyzeR object is provided, this parameter is not needed.
- variable
The name of the variable in the metadata contain information for sex. Default is "Sex".
- sex
The value of the sex variable to filter by.
Examples
# Create the HDAnalyzeR object providing the data and metadata
hd_object <- hd_initialize(example_data, example_metadata)
hd_filter_by_sex(hd_object, variable = "Sex", sex = "F")
#> $data
#> # A tibble: 366 × 101
#> DAid AARSD1 ABL1 ACAA1 ACAN ACE2 ACOX1 ACP5 ACP6 ACTA2 ACTN4
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 DA00… 3.39 2.76 1.71 0.0333 1.76 -0.919 1.54 2.15 2.81 0.742
#> 2 DA00… NA NA NA 0.989 NA 0.330 1.37 NA NA NA
#> 3 DA00… 5.01 5.05 0.128 0.401 -0.933 -0.584 0.0265 1.16 2.73 0.350
#> 4 DA00… NA NA 3.96 0.682 3.14 2.62 1.47 2.25 2.01 0.170
#> 5 DA00… 2.78 0.812 -0.552 0.982 -0.101 -0.304 0.376 -0.826 1.52 -0.597
#> 6 DA00… 3.48 4.96 3.50 -0.338 4.48 1.26 2.18 1.62 1.79 0.233
#> 7 DA00… 4.31 0.710 -1.44 -0.218 -0.469 -0.361 -0.0714 -1.30 2.86 0.129
#> 8 DA00… 1.79 1.36 0.106 -0.372 3.40 -1.19 1.77 1.07 2.00 0.980
#> 9 DA00… 3.59 3.38 1.79 -0.303 1.59 0.604 1.71 -0.837 1.65 1.13
#> 10 DA00… 1.80 1.70 2.77 -1.04 1.33 -0.0247 1.02 0.112 2.58 1.14
#> # ℹ 356 more rows
#> # ℹ 90 more variables: ACY1 <dbl>, ADA <dbl>, ADA2 <dbl>, ADAM15 <dbl>,
#> # ADAM23 <dbl>, ADAM8 <dbl>, ADAMTS13 <dbl>, ADAMTS15 <dbl>, ADAMTS16 <dbl>,
#> # ADAMTS8 <dbl>, ADCYAP1R1 <dbl>, ADGRE2 <dbl>, ADGRE5 <dbl>, ADGRG1 <dbl>,
#> # ADGRG2 <dbl>, ADH4 <dbl>, ADM <dbl>, AGER <dbl>, AGR2 <dbl>, AGR3 <dbl>,
#> # AGRN <dbl>, AGRP <dbl>, AGXT <dbl>, AHCY <dbl>, AHSP <dbl>, AIF1 <dbl>,
#> # AIFM1 <dbl>, AK1 <dbl>, AKR1B1 <dbl>, AKR1C4 <dbl>, AKT1S1 <dbl>, …
#>
#> $metadata
#> # A tibble: 366 × 9
#> DAid Sample Disease Stage Grade Sex Age BMI Cohort
#> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <chr>
#> 1 DA00001 AML_syn_1 AML 2 NA F 42 22.7 UCAN
#> 2 DA00003 AML_syn_3 AML 2 NA F 61 26.2 UCAN
#> 3 DA00005 AML_syn_5 AML 2 NA F 57 21.4 UCAN
#> 4 DA00007 AML_syn_7 AML 1 NA F 85 28.7 UCAN
#> 5 DA00008 AML_syn_8 AML 3 NA F 88 32.6 UCAN
#> 6 DA00011 AML_syn_11 AML 3 NA F 54 34.7 UCAN
#> 7 DA00012 AML_syn_12 AML 3 NA F 78 21.4 UCAN
#> 8 DA00016 AML_syn_16 AML 3 NA F 78 25.4 UCAN
#> 9 DA00019 AML_syn_19 AML 1 NA F 81 22.9 UCAN
#> 10 DA00020 AML_syn_20 AML 3 NA F 65 24.1 UCAN
#> # ℹ 356 more rows
#>
#> $sample_id
#> [1] "DAid"
#>
#> $var_name
#> [1] "Assay"
#>
#> $value_name
#> [1] "NPX"
#>
#> attr(,"class")
#> [1] "HDAnalyzeR"