CLK1 exon 4 variation

[naqvia]

Compute variation for CLK1 Exon 4 in samples with high CLK1 expression

[naqvia]

To summarize the tpm isoform plot. There are 32 tumors that are > .8239 (highest pediatric percentage -- frontal cortex).

# A tibble: 9 × 2
  plot_group                     n
  <fct>                      <int>
1 Craniopharyngioma              3
2 Ependymoma                    11
3 Choroid plexus tumor           2
4 Mesenchymal tumor              2
5 Low-grade glioma               9
6 Schwannoma                     1
7 Medulloblastoma                1
8 Mixed neuronal-glial tumor     2
9 DIPG or DMG                    1

There are 15 HGGs that are greater than the Pons ctrl.

We can argue that these may be unusually elevated with CLK1 Ex 4 transcripts.

[jharenza]

hey @naqvia this seems almost ready - can you delete the plots and rerun the entire module once scripts 11-12 paths are updated - i think there may be some old plots lying around.

[naqvia]

Please review when you can, and will merge. Will the work on the last remaining PRs.

[naqvia]

Please review and merge. @jharenza

[jharenza]

Rscript --vanilla 11-plot-clk1-ex4-transcripts-by-age-gtex.R

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

Error in library(coin) : there is no package called ‘coin’
Execution halted

[jharenza]

also

Rscript --vanilla 12-plot-clk1-ex4-transcripts-by-age.R
Rows: 12772 Columns: 6
── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (6): Kids_First_Participant_ID, Kids_First_Biospecimen_ID, cohort, cance...

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.
Rows: 8489 Columns: 65
── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (44): Kids_First_Participant_ID, Kids_First_Biospecimen_ID, sample_id, a...
dbl (17): OS_days, EFS_days, age_at_diagnosis_days, age_at_event_days, age_a...
lgl (4): cell_line_composition, cell_line_passage, gtex_group, gtex_subgroup

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.
Error: object 'expr_tpm_tumor_file' not found
Execution halted

[naqvia]

Fixed the file issue. Coin library needs to be installed, so will make a Docker update that would need to address this

[naqvia]

Please review and merge #24 and then re-run this module.

[jharenza]

all good now