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Se realizará un ejemplo de análisis de datos Chunk : cmd + option + I

Instalación de paquetes

#install.packages("pacman") 
library("pacman") 

p_load("ggplot2", 
       "dplyr", 
       "vroom")

Llamar a base de datos

Datos_PCR <- vroom(file = "https://raw.githubusercontent.com/ManuelLaraMVZ/resultados_PCR_practica/refs/heads/main/Genes.csv")
## Rows: 7 Columns: 7
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (1): Gen
## dbl (6): C1, C2, C3, T1, T2, T3
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Datos_PCR
## # A tibble: 7 × 7
##   Gen         C1    C2    C3    T1    T2    T3
##   <chr>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 B-actina  19    19.5  18.9  18.5  18.8  18.2
## 2 PIF1      22.4  22    21    28    28.2  27.9
## 3 PLK1      22    21.8  21.6  21.7  21    21.5
## 4 CCNB1     30.1  31.2  30.8  25.2  25.2  25.3
## 5 PCNA      20    20.3  20.2  24    24.2  NA  
## 6 CCNB2     33    NA    33.1  24    25    26  
## 7 BRCA      21    20.5  20.4  19.1  19.2  19.5

Aislar los genes de referencia para cada condición

Gen_ref <- Datos_PCR %>%
  filter(Gen == "B-actina")

Gen_ref
## # A tibble: 1 × 7
##   Gen         C1    C2    C3    T1    T2    T3
##   <chr>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 B-actina    19  19.5  18.9  18.5  18.8  18.2

Generar base de datos con genes de interés

Gen_int <- Datos_PCR %>%
  filter (Gen != "B-actina")

Gen_int
## # A tibble: 6 × 7
##   Gen      C1    C2    C3    T1    T2    T3
##   <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 PIF1   22.4  22    21    28    28.2  27.9
## 2 PLK1   22    21.8  21.6  21.7  21    21.5
## 3 CCNB1  30.1  31.2  30.8  25.2  25.2  25.3
## 4 PCNA   20    20.3  20.2  24    24.2  NA  
## 5 CCNB2  33    NA    33.1  24    25    26  
## 6 BRCA   21    20.5  20.4  19.1  19.2  19.5

Realizar análisis

DCT <- Gen_int %>%
  # calcular DCT
  mutate(DC1 = C1 - Gen_ref$C1,
         DC2 = C2 - Gen_ref$C2,
         DC3 = C3 - Gen_ref$C3,
         DT1 = T1 - Gen_ref$T1,
         DT2 = T2 - Gen_ref$T2,
         DT3 = T3 - Gen_ref$T3) %>%
  # calcular 2^DCT
  mutate(DosDCTC1 = 2^-DC1,
         DosDCTC2 = 2^-DC2,
         DosDCTC3 = 2^-DC3,
         DosDCTT1 = 2^-DT1,
         DosDCTT2 = 2^-DT2,
         DosDCTT3 = 2^-DT3) %>% 
  # promediar 3 réplicas (tratamiento y control)
  mutate(DosDCTCx = (DosDCTC1 + DosDCTC2 + DosDCTC3)/3) %>% 
  mutate(DosDCTTx = (DosDCTT1 + DosDCTT2 + DosDCTT3)/3) %>% 
  # calcular 2^DDCT
  mutate(DosDDCT = DosDCTTx/DosDCTCx)

DCT
## # A tibble: 6 × 22
##   Gen      C1    C2    C3    T1    T2    T3   DC1    DC2   DC3   DT1   DT2   DT3
##   <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>  <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 PIF1   22.4  22    21    28    28.2  27.9   3.4  2.5    2.08 9.5   9.45    9.7
## 2 PLK1   22    21.8  21.6  21.7  21    21.5   3    2.3    2.68 3.2   2.25    3.3
## 3 CCNB1  30.1  31.2  30.8  25.2  25.2  25.3  11.1 11.7   11.9  6.7   6.45    7.1
## 4 PCNA   20    20.3  20.2  24    24.2  NA     1    0.800  1.28 5.5   5.45   NA  
## 5 CCNB2  33    NA    33.1  24    25    26    14   NA     14.2  5.5   6.25    7.8
## 6 BRCA   21    20.5  20.4  19.1  19.2  19.5   2    1      1.48 0.600 0.450   1.3
## # ℹ 9 more variables: DosDCTC1 <dbl>, DosDCTC2 <dbl>, DosDCTC3 <dbl>,
## #   DosDCTT1 <dbl>, DosDCTT2 <dbl>, DosDCTT3 <dbl>, DosDCTCx <dbl>,
## #   DosDCTTx <dbl>, DosDDCT <dbl>

Gráfica

Datos_grafica <- DCT %>% 
  select("Gen","DosDDCT")
Datos_grafica
## # A tibble: 6 × 2
##   Gen    DosDDCT
##   <chr>    <dbl>
## 1 PIF1   0.00790
## 2 PLK1   0.869  
## 3 CCNB1 27.7    
## 4 PCNA  NA      
## 5 CCNB2 NA      
## 6 BRCA   1.62
Grafica_PCR <-  ggplot(Datos_grafica,
                       mapping = aes(x = Gen,
                                     y = DosDDCT)) +
  geom_col() + 
  theme_classic()

Grafica_PCR
## Warning: Removed 2 rows containing missing values or values outside the scale range
## (`geom_col()`).

Gráfica de regresión lineal

Generar nueva base de datos a partir de la de DCT (solo los promedios de 2^-DCTCx y 2^-DCTTx)

Datos_regresion <- DCT %>% 
  select("Gen", "DosDCTCx", "DosDCTTx")

Datos_regresion
## # A tibble: 6 × 3
##   Gen    DosDCTCx DosDCTTx
##   <chr>     <dbl>    <dbl>
## 1 PIF1   0.169     0.00134
## 2 PLK1   0.161     0.140  
## 3 CCNB1  0.000340  0.00945
## 4 PCNA   0.495    NA      
## 5 CCNB2 NA         0.0132 
## 6 BRCA   0.369     0.599

Graficar regresión (y = Tx, x = Cx)

Grafica_regresion <- ggplot(Datos_regresion,
                            aes(x = DosDCTCx,
                                y = DosDCTTx)) +
  geom_point(color = "#2E86AB", size = 3.5, alpha = 0.8, shape = 16) + 
  # Línea de referencia (pendiente 1) 
  geom_abline(intercept = 0, slope = 1, color = "#E74C3C", linetype = "dashed", size = 1.2) + 
  # Línea de regresión calculada 
  theme_minimal(base_size = 15, base_family = "serif") + 
  
  labs( 
    title = "Regresión", 
    subtitle = "Comparación entre 2^CTCx y 2^DCTTx", 
    x = "2^DCTCx", 
    y = "2^DCTCx" )
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
Grafica_regresion
## Warning: Removed 2 rows containing missing values or values outside the scale range
## (`geom_point()`).