Exercises-05

Sujatha Jagannathan

RNA Bioscience Initiative | CU Anschutz

2020-08-28

R bootcamp review

# A tibble: 600 × 5
# Groups:   type [1]
   ensembl_transcript_id      type  time  replicate count
   <chr>                      <chr> <chr> <chr>     <dbl>
 1 ENST00000327044.6_51_2298  rna   0h    rep1        243
 2 ENST00000327044.6_51_2298  rna   0h    rep2        322
 3 ENST00000327044.6_51_2298  rna   0h    rep3        303
 4 ENST00000327044.6_51_2298  rna   14h   rep1        177
 5 ENST00000327044.6_51_2298  rna   14h   rep2        177
 6 ENST00000327044.6_51_2298  rna   14h   rep3        239
 7 ENST00000338591.7_360_2034 rna   0h    rep1         19
 8 ENST00000338591.7_360_2034 rna   0h    rep2         17
 9 ENST00000338591.7_360_2034 rna   0h    rep3         15
10 ENST00000338591.7_360_2034 rna   14h   rep1          9
# ℹ 590 more rows

# A tibble: 600 × 5
# Groups:   replicate [3]
   ensembl_transcript_id      type  time  replicate count
   <chr>                      <chr> <chr> <chr>     <dbl>
 1 ENST00000327044.6_51_2298  rna   0h    rep1        243
 2 ENST00000327044.6_51_2298  rna   0h    rep2        322
 3 ENST00000327044.6_51_2298  rna   0h    rep3        303
 4 ENST00000327044.6_51_2298  rna   14h   rep1        177
 5 ENST00000327044.6_51_2298  rna   14h   rep2        177
 6 ENST00000327044.6_51_2298  rna   14h   rep3        239
 7 ENST00000338591.7_360_2034 rna   0h    rep1         19
 8 ENST00000338591.7_360_2034 rna   0h    rep2         17
 9 ENST00000338591.7_360_2034 rna   0h    rep3         15
10 ENST00000338591.7_360_2034 rna   14h   rep1          9
# ℹ 590 more rows

# A tibble: 600 × 5
# Groups:   time [2]
   ensembl_transcript_id      type  time  replicate count
   <chr>                      <chr> <chr> <chr>     <dbl>
 1 ENST00000327044.6_51_2298  rna   0h    rep1        243
 2 ENST00000327044.6_51_2298  rna   0h    rep2        322
 3 ENST00000327044.6_51_2298  rna   0h    rep3        303
 4 ENST00000327044.6_51_2298  rna   14h   rep1        177
 5 ENST00000327044.6_51_2298  rna   14h   rep2        177
 6 ENST00000327044.6_51_2298  rna   14h   rep3        239
 7 ENST00000338591.7_360_2034 rna   0h    rep1         19
 8 ENST00000338591.7_360_2034 rna   0h    rep2         17
 9 ENST00000338591.7_360_2034 rna   0h    rep3         15
10 ENST00000338591.7_360_2034 rna   14h   rep1          9
# ℹ 590 more rows

# A tibble: 600 × 5
# Groups:   ensembl_transcript_id [100]
   ensembl_transcript_id      type  time  replicate count
   <chr>                      <chr> <chr> <chr>     <dbl>
 1 ENST00000327044.6_51_2298  rna   0h    rep1        243
 2 ENST00000327044.6_51_2298  rna   0h    rep2        322
 3 ENST00000327044.6_51_2298  rna   0h    rep3        303
 4 ENST00000327044.6_51_2298  rna   14h   rep1        177
 5 ENST00000327044.6_51_2298  rna   14h   rep2        177
 6 ENST00000327044.6_51_2298  rna   14h   rep3        239
 7 ENST00000338591.7_360_2034 rna   0h    rep1         19
 8 ENST00000338591.7_360_2034 rna   0h    rep2         17
 9 ENST00000338591.7_360_2034 rna   0h    rep3         15
10 ENST00000338591.7_360_2034 rna   14h   rep1          9
# ℹ 590 more rows

# A tibble: 1 × 1
  count
  <dbl>
1  144.

# A tibble: 2 × 2
  time  count
  <chr> <dbl>
1 0h     185.
2 14h    103.

# A tibble: 100 × 2
   ensembl_transcript_id          count
   <chr>                          <dbl>
 1 ENST00000054650.8_159_876       8.39
 2 ENST00000054666.10_116_416    121.  
 3 ENST00000054668.5_220_418       3.75
 4 ENST00000234590.8_121_1423   7993.  
 5 ENST00000263741.11_1328_1496   29.4 
 6 ENST00000263741.11_315_1338   141.  
 7 ENST00000270708.11_75_1455     45.7 
 8 ENST00000288774.7_29_1067      16.1 
 9 ENST00000291386.3_370_895     134.  
10 ENST00000307896.10_39_753       8.39
# ℹ 90 more rows

# A tibble: 200 × 3
# Groups:   ensembl_transcript_id [100]
   ensembl_transcript_id        time    count
   <chr>                        <chr>   <dbl>
 1 ENST00000054650.8_159_876    0h       11.3
 2 ENST00000054650.8_159_876    14h       5.5
 3 ENST00000054666.10_116_416   0h      149  
 4 ENST00000054666.10_116_416   14h      93.7
 5 ENST00000054668.5_220_418    0h        0  
 6 ENST00000054668.5_220_418    14h       7.5
 7 ENST00000234590.8_121_1423   0h    10522. 
 8 ENST00000234590.8_121_1423   14h    5465. 
 9 ENST00000263741.11_1328_1496 0h       32.5
10 ENST00000263741.11_1328_1496 14h      26.3
# ℹ 190 more rows

• functions to use within mutate - google is your friend

• manipulation of cols & rows - use cheatsheets

• ggplot

  • aesthetic mapping: Ref

• piping data into ggplot - example below

• more applied examples - plenty to come in the rest of the course

• specifying colors of plots: tutorial

• other
  • log10 - ?log10
  • How to use Help pages: help()
  • required vs. optional arguments: this is possible to distinguish if you have a well-documented function. If not, trial-an-error is how it goes.
  • Use of commas with multiple vars: Depends on the function. Look at the exact syntax required for specific functions on the cheatsheet to know what to use: col1, col2, col3, vs col1:col3, etc
  • Metacharacters “.” etc.: Refer to cheatsheet on Regex + stringr