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Affection and availability information table

Source: R/app_ped_avaf_infos.R
family_infos_table.Rd

This function creates a table with the affection and availability information for all individuals in a pedigree object.

Usage

family_infos_table(pedi, col_val = NA)

Arguments

pedi

A pedigree object.

col_val

The column name in the fill slot of the pedigree object to use for the table.

Value

A cross table dataframe with the affection and availability information.

Examples

data(sampleped)
pedi <- Pedigree(sampleped)
#>    id dadid momid famid 
#> "101"    NA    NA   "1" 
#>    id dadid momid famid 
#> "102"    NA    NA   "1" 
#>    id dadid momid famid 
#> "103" "135" "136"   "1" 
#>    id dadid momid famid 
#> "104"    NA    NA   "1" 
#>    id dadid momid famid 
#> "105"    NA    NA   "1" 
#>    id dadid momid famid 
#> "106"    NA    NA   "1" 
#>    id dadid momid famid 
#> "107"    NA    NA   "1" 
#>    id dadid momid famid 
#> "108"    NA    NA   "1" 
#>    id dadid momid famid 
#> "109" "101" "102"   "1" 
#>    id dadid momid famid 
#> "110" "103" "104"   "1" 
#>    id dadid momid famid 
#> "111" "103" "104"   "1" 
#>    id dadid momid famid 
#> "112" "103" "104"   "1" 
#>    id dadid momid famid 
#> "113"    NA    NA   "1" 
#>    id dadid momid famid 
#> "114" "103" "104"   "1" 
#>    id dadid momid famid 
#> "115" "105" "106"   "1" 
#>    id dadid momid famid 
#> "116" "105" "106"   "1" 
#>    id dadid momid famid 
#> "117"    NA    NA   "1" 
#>    id dadid momid famid 
#> "118" "105" "106"   "1" 
#>    id dadid momid famid 
#> "119" "105" "106"   "1" 
#>    id dadid momid famid 
#> "120" "107" "108"   "1" 
#>    id dadid momid famid 
#> "121" "110" "109"   "1" 
#>    id dadid momid famid 
#> "122" "110" "109"   "1" 
#>    id dadid momid famid 
#> "123" "110" "109"   "1" 
#>    id dadid momid famid 
#> "124" "110" "109"   "1" 
#>    id dadid momid famid 
#> "125" "112" "118"   "1" 
#>    id dadid momid famid 
#> "126" "112" "118"   "1" 
#>    id dadid momid famid 
#> "127" "114" "115"   "1" 
#>    id dadid momid famid 
#> "128" "114" "115"   "1" 
#>    id dadid momid famid 
#> "129" "117" "116"   "1" 
#>    id dadid momid famid 
#> "130" "119" "120"   "1" 
#>    id dadid momid famid 
#> "131" "119" "120"   "1" 
#>    id dadid momid famid 
#> "132" "119" "120"   "1" 
#>    id dadid momid famid 
#> "133" "119" "120"   "1" 
#>    id dadid momid famid 
#> "134" "119" "120"   "1" 
#>    id dadid momid famid 
#> "135"    NA    NA   "1" 
#>    id dadid momid famid 
#> "136"    NA    NA   "1" 
#>    id dadid momid famid 
#> "137"    NA    NA   "1" 
#>    id dadid momid famid 
#> "138" "135" "136"   "1" 
#>    id dadid momid famid 
#> "139" "137" "138"   "1" 
#>    id dadid momid famid 
#> "140" "137" "138"   "1" 
#>    id dadid momid famid 
#> "141" "137" "138"   "1" 
#>    id dadid momid famid 
#> "201"    NA    NA   "2" 
#>    id dadid momid famid 
#> "202"    NA    NA   "2" 
#>    id dadid momid famid 
#> "203"    NA    NA   "2" 
#>    id dadid momid famid 
#> "204" "201" "202"   "2" 
#>    id dadid momid famid 
#> "205" "201" "202"   "2" 
#>    id dadid momid famid 
#> "206" "201" "202"   "2" 
#>    id dadid momid famid 
#> "207" "201" "202"   "2" 
#>    id dadid momid famid 
#> "208" "201" "202"   "2" 
#>    id dadid momid famid 
#> "209"    NA    NA   "2" 
#>    id dadid momid famid 
#> "210" "203" "204"   "2" 
#>    id dadid momid famid 
#> "211" "203" "204"   "2" 
#>    id dadid momid famid 
#> "212" "209" "208"   "2" 
#>    id dadid momid famid 
#> "213" "209" "208"   "2" 
#>    id dadid momid famid 
#> "214" "209" "208"   "2" 
pedi <- generate_colors(pedi, "num_child_tot", threshold = 2)
#> Warning: 1_1141_117 individual(s) are/is proband but not affected
#> Warning: 1_109 individual(s) are/is asymptomatic but affected
#> Warning: 1_1141_117 individual(s) are/is proband but not affected
#> Warning: 1_109 individual(s) are/is asymptomatic but affected
Pedixplorer:::family_infos_table(pedi, "num_child_tot")
#>   Affected            mods TRUE FALSE NA
#> 1        0 Healthy <= to 2   20    21  0
#> 2        1 Affected > to 2    4    10  0
#> 3       NA              NA    0     0  0
Pedixplorer:::family_infos_table(pedi, "affection")
#>   Affected              mods TRUE FALSE NA
#> 1        0 Healthy <= to 0.5   11    12  0
#> 2        1 Affected > to 0.5   12    10  0
#> 3       NA                NA    1     9  0