Fix error in get_ssm_by_samples function

[vladimirsouza]

get_ssm_by_samples function uses parallel::mclapply internally. But it neither import mclapply nor add parallel:: prefix to mclapply. Hence, the error

could not find function "mclapply"

may be returned (which could be avoided by running library(parallel) before calling get_ssm_by_samples).

Other functions that use get_ssm_by_samples internally (e.g. get_ssm_by_patients) return the same error.

Add parallel:: prefix to mclapply.

Pull Request Checklists

Checklist for all PRs

Required

• [x] I tested the new code for my use case (please provide a reproducible example of how you tested the new functionality)

library(GAMBLR)

#set sample IDs
these_samples = c("HTMCP-01-06-00485-01A-01D", 
                  "14-35472_tumorA", 
                  "14-35472_tumorB")

#get_ssm_by_samples
these_samples_ssm = get_ssm_by_samples(these_sample_ids = these_samples,
                                       projection = "grch37",
                                       seq_type = "genome")

#set patient IDs
these_patients = c("00-14595", 
                   "00-15201", 
                   "01-12047")

#get_ssm_by_patients
these_patients_ssm = get_ssm_by_patients(these_patient_ids = these_patients,
                                         seq_type = "genome",
                                         projection = "grch37")

Visualization of the these_samples_ssm object:

> head(these_samples_ssm, 3)
   Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position
1:     Unknown              0      .     GRCh37          1        5507023
2:      CAMTA1              0      .     GRCh37          1        7304379
3:        PER3              0      .     GRCh37          1        7888519
   End_Position Strand Variant_Classification Variant_Type Reference_Allele
1:      5507023      +                    IGR          SNP                C
2:      7304379      +                 Intron          SNP                G
3:      7888519      +                 Intron          SNP                G
   Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status
1:                 C                 G    novel               NA
2:                 G                 A    novel               NA
3:                 G                 A    novel               NA
        Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1
1: HTMCP-01-06-00485-01A-01D   HTMCP-01-06-00485-12B-01D                      C
2: HTMCP-01-06-00485-01A-01D   HTMCP-01-06-00485-12B-01D                      G
3: HTMCP-01-06-00485-01A-01D   HTMCP-01-06-00485-12B-01D                      G
   Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2
1:                      C                       NA                       NA
2:                      G                       NA                       NA
3:                      G                       NA                       NA
   Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2
1:                            NA                            NA
2:                            NA                            NA
3:                            NA                            NA
   Verification_Status Validation_Status Mutation_Status Sequencing_Phase
1:                  NA                NA              NA               NA
2:                  NA                NA              NA               NA
3:                  NA                NA              NA               NA
   Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID
1:              NA                NA    NA       NA        NA                NA
2:              NA                NA    NA       NA        NA                NA
3:              NA                NA    NA       NA        NA                NA
   Matched_Norm_Sample_UUID         HGVSc HGVSp HGVSp_Short   Transcript_ID
1:                       NA                                                
2:                       NA c.303-5172G>A                   ENST00000303635
3:                       NA c.2862+644G>A                   ENST00000361923
   Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count
1:                  66          33          33      40          40           0
2:                  74          37          36      34          34           0
3:                  70          29          41      33          33           0

• [x] I ensured all dplyr functions that commonly conflict with other packages are fully qualified.

• [x] I generated the documentation and checked for errors relating to the changed function (e.g. devtools::document()) and added NAMESPACE and all other modified files in the root directory and under man.

• [ ] I have rebuilt the site with pkgdown::build_site(lazy = TRUE) to reflect any updated package documentation.

Optional but preferred with PRs

Checklist for New Functions

Required

• [x] I changed an existing function and now it uses a library that isn't already a dependency of GAMBLR and I made the package aware of this dependency using the function documentation importFrom statement.

[vladimirsouza]

Please, notice that I didn't check the pkgdown::build_site step of the checklist, since it is not working for me. See error message in this slack discussion.

[vladimirsouza]

I updated this branch to contain the last pushes to master.